Table 1.

Bioinformatics tools.

	Tool	Reference
	ARG-ANNOT	[20]
	CARD/RGI	[21]
ARGs	AMRFinder	[22]
	ResFinder	[23]
	PointFinder	[24]
	Fastp	[25]
Preprocessing and assembly-WGS	SPAdes/	[26]
	Flye	[27]
	Mzmine3	[28]
	MetaboAnalyst 5.0	[29]
Metabolomic analysis	MetFlow	[30]
	Omicsnet	[31]
	PaintOmics 3	[32]
	DESeq	[33]
	edgeR	[34]
General tools for transcriptomic analysis	limma	[35]
	HTseq	[36]
	Rcount	[37]
	Cufflinks-Cuffdiff	[38]
	BioCyc	[39]
	BioMet ToolBox 2.0	[40]
GEM reconstruction	Kegg	[41]
	GeneOntology	[42]
	Pathway-tools	[43]
GEM analysis	CobraToolbox	[44]