Adjacency matrix	Matrix representation of network connections
ARI	Adjusted Rand Index, clustering agreement measure adjusted for chance
B-BGM	Bergen Brain–Gut Microbiota project
Betweenness centrality	Measure of how often a node lies on shortest paths between other nodes
Bootstrap	Resampling method for estimating confidence intervals
CBT	Cognitive Behavioral Therapy
CC	Corpus Callosum
CI	Confidence Interval
Community	Group of nodes more densely connected to
	each other than to the rest of the network
Degree centrality	Normalized measure of node connectivity
DGBI	Disorder of Gut–Brain Interaction
Edge	Connection between two nodes representing patient similarity
Eigenvector centrality	Node importance based on connections to other important nodes
eTIV	Estimated total intracranial volume
FDR	False Discovery Rate, correction for multiple testing
FODMAP	Fermentable Oligosaccharides, Disaccharides,
	Monosaccharides, and Polyols
FreeSurfer	Neuroimaging software for brain segmentation and volumetric analysis
Gaussian kernel	Function transforming distances to similarities
GI	Gastrointestinal
Graph/Network	Mathematical structure of nodes connected by edges
HC	Healthy Controls
IBS	Irritable Bowel Syndrome
IBS-C/-D/-M	IBS subtypes: constipation-predominant, diarrhea-predominant, mixed
IBS-SSS	IBS Severity Scoring System (range 0–500)
k-NN	k-nearest neighbors, network construction method
Louvain algorithm	Greedy algorithm for community detection via modularity maximization
MDCP	The Rome Foundation’s Multidimensional Clinical Profile
MRI	Magnetic Resonance Imaging
Modularity (Q)	Measure of network partition quality
Network density	Proportion of possible edges present in the network
Network sparsification	Process of removing weak edges
NICE	National Institute for Health and Care Excellence
NMI	Normalized Mutual Information, clustering similarity measure
Node	Vertex in the network representing an individual patient
Node degree	Number of edges connected to a node
Permutation test	Non-parametric method using random label shuffling
PSN	Patient Similarity Network
RBANS	Repeatable Battery for the Assessment of Neuropsychological Status
SD	Standard Deviation
Similarity matrix	Matrix containing pairwise similarity values between patients
Similarity threshold	Minimum similarity for edge inclusion
SNF	Similarity Network Fusion
Weighted edge	Edge with numerical value representing similarity strength