AMR	Antimicrobial resistance
AP-MS	Affinity purification–mass spectrometry
B2H	Bacterial two-hybrid
DBG	de Bruijn graph
DDA	Data-dependent acquisition
DIA	Data-independent acquisition
DRS	Direct RNA sequencing
FACS	Fluorescence-activated cell sorting
GWAS	Genome-wide association studies
LD	Linkage disequilibrium
LMM	Linear mixed models
MDS	Multidimensional scaling
ONT	Oxford nanopore technology
PCA	Principal component analysis
PL	Proximity labeling
PPI	Protein–protein interaction
PTM	Post-translational modification
QTL	Quantitative trait locus
SBP	Single-bacterium proteomics
SNP	Single-nucleotide polymorphism
SVM	Support vector machine
TDP	Top-down proteomics
TRIPs	Transcription–replication interaction profiles
XL-MS	Cross-linking mass spectrometry
Y2H	Yeast two-hybrid