Abbreviation	Expansion
PROBAT	Probiotics in the Prevention of Atopy in Infants and Children
SP	starting point
EP	endpoint
CST	community state type
IQR	interquartile range
AOR	adjusted odds ratio
CFU	colony-forming units
gDNA	genomic DNA
ASV	amplicon sequence variant
16S rDNA	16S ribosomal DNA
CLR	centre-log-ratio
ARG	antibiotic-resistance gene
MGE	mobile genetic element
ORF	open reading frame
RPKM	reads per kilobase per million mapped reads
PCoA	principal coordinates analysis
NMDS	non-metric multidimensional scaling
JSD	Jensen–Shannon Divergence
GLMM	generalised linear mixed model
AIC	Akaike information criterion
FDR	false discovery rate
DADA2	Divisive Amplicon Denoising Algorithm 2
NCIMB	National Collection of Industrial, Food and Marine Bacteria
CARD	Comprehensive Antibiotic Resistance Database
RGI	Resistance Gene Identifier
DESeq2	Differential Expression Sequencing version 2
HUMAnN	The HMP Unified Metabolic Analysis Network
MetaCyc	metabolic pathway database
CHOCOPhlAn	A pan-genome database used with MetaPhlAn
NetCoMi	Network Construction and Comparison for Microbiome Data