holobiont (version 0.1.3)

coreEdges: Edges of the Tree Included in the Core Community Phylogeny

Description

Finds the edges of a phylogenetic tree that are part of the core microbiome based on either the tip-based or the branch-based core community phylogeny.

Usage

coreEdges(x, core_fraction = 0.5, ab_threshold1 = 0,
ab_threshold2 = 0, ab_threshold3 = 0, mode='branch',
selection='basic', max_tax = NULL, increase_cutoff = 2,
initial_branches = NULL, rooted=TRUE, remove_zeros=TRUE)

Value

This function returns a list of the edges of the phylogenetic tree associated with the core microbiome.

Arguments

x

(Required) Microbial community data. This must be in the form of a phyloseq object and must contain, at a minimum, an OTU abundance table and a phylogeny.

core_fraction

The fraction of samples that a microbial taxon must be found in to be considered part of the 'core' microbiome. This variable is only used when selection = 'basic' and is ignored when selection = 'shade'. The default value is 0.5.

ab_threshold1

The threshold for mean relative abundance across all samples. This variable is only used when selection = 'basic' and is ignored when selection = 'shade'. The default value is 0.

ab_threshold2

The threshold for maximum relative abundance in any sample. This variable is only used when selection = 'basic' and is ignored when selection = 'shade'. The default value is 0.

ab_threshold3

The threshold for minimum relative abundance across all samples. This variable is only used when selection = 'basic' and is ignored when selection = 'shade'. The default value is 0.

mode

Whether to build a tip-based ('tip') or a branch-based ('branch') phylogeny. The default is 'branch'.

selection

Whether to use thresholds ('basic') or the Shade and Stopnisek method ('shade') to define the core community. The default is 'basic'.

max_tax

The maximum number of branches to add sequentially, as a percentage of the total branches when using the Shade and Stopnisek method. This variable is only used when selection = 'shade' and is ignored when selection = 'basic'.

increase_cutoff

The threshold for the percent increase in beta diversity used to identify the taxon at which point adding more taxa yields diminishing returns in explanatory power. This variable is only used when selection = 'shade' and is ignored when selection = 'basic'.

initial_branches

The number of branches to include prior to testing for increases in beta diversity. The default is to use all branches that are present in every sample and to begin testing branches that are missing from at least one sample. This variable is only used when selection = 'shade' and is ignored when selection = 'basic'.

rooted

Whether to include the root of the phylogeny. The default is TRUE, meaning that the root is necessarily included in all phylogenies. This requires that the input tree be rooted.

remove_zeros

Whether or not to remove taxa that are no reads associated across any of the samples.

Details

coreEdges identifies the edges of the core community phylogeny based on either the tip-based or the branch-based core community phylogeny using either basic thresholds or a modification of the Shade and Stopnisek (2019) algorithm. For more details, see Bewick and Camper (2025).

References

Shade, Ashley, and Nejc Stopnisek. "Abundance-occupancy distributions to prioritize plant core microbiome membership." Current opinion in microbiology 49 (2019): 50-58.

Examples

#Test with enterotype dataset
library(phyloseq)
library(ape)
library(phytools)
data(enterotype)

set.seed(1)

#Generate an example tree and label it with the names of the microbial taxa
enterotype_tree<-rtree(length(taxa_names(enterotype)))
enterotype_tree$tip.label<-taxa_names(enterotype)
enterotype_tree$node.label<-as.character(1:1:enterotype_tree$Nnode)

#Create a phyloseq object with a tree
example_phyloseq<-phyloseq(otu_table(enterotype),phy_tree(as.phylo(enterotype_tree)))

coreEdges(example_phyloseq)