AMP	adenosine monophosphate
AMPK	AMP-activated protein kinase
BBR	berberine
BGISEQ-500	Beijing Genomics Institute sequencing platform 500
BLASTP	Basic Local Alignment Search Tool (protein)
BLASTX	Basic Local Alignment Search Tool (translated nucleotide)
BMI	body mass index
CCN4	cellular communication network factor 4
FBG	fasting blood glucose
FLASH	Fast Length Adjustment of Short Reads
FPI	fasting plasma insulin
FPG	fasting plasma glucose
FXR	farnesoid X receptor
GLP-1	glucagon-like peptide-1
HbA1c	glycated haemoglobin
HDL-C	high-density lipoprotein cholesterol
HOMA-β	homeostatic model assessment of beta-cell function
HOMA-IR	homeostatic model assessment of insulin resistance
IGC	integrated gene catalogue
IL-6	interleukin-6
IL-8	interleukin-8
KEGG	Kyoto Encyclopedia of Genes and Genomes
KO	KEGG Orthology
LDA	linear discriminant analysis
LDL-C	low-density lipoprotein cholesterol
LDLR	low-density lipoprotein receptor
LEfSe	linear discriminant analysis effect size
LPS	lipopolysaccharide
NCBI	National Center for Biotechnology Information
NF-κB	nuclear factor kappa B
NOD2	nucleotide oligomerization domain 2
NR	NCBI non-redundant protein database
OTU	operational taxonomic unit
PCR	polymerase chain reaction
PCoA	principal coordinates analysis
PCSK9	proprotein convertase subtilisin/kexin type 9
PICOS	Population, Intervention, Comparison, Outcome, Study design
PLS-DA	partial least squares discriminant analysis
PRISMA	Preferred Reporting Items for Systematic Reviews and Meta-Analyses
PROSPERO	International Prospective Register of Systematic Reviews
qPCR	quantitative polymerase chain reaction
QIIME	Quantitative Insights Into Microbial Ecology
RCT	randomised controlled trial
RDP	Ribosomal Database Project
RNA	ribonucleic acid
ROB	Risk of Bias tool
SCFA	short-chain fatty acid
SGLT1	sodium-glucose cotransporter 1
SILVA	Ribosomal RNA sequence database
SOAP2	Short Oligonucleotide Analysis Package version 2
T2DM	type 2 diabetes mellitus
TC	total cholesterol
TG	triglycerides
TGR5	Takeda G protein-coupled receptor 5
TLR4	Toll-like receptor 4
TMAO	trimethylamine N-oxide
TNF-α	tumour necrosis factor-alpha
UCLUST	USEARCH clustering algorithm
USEARCH	ultrafast sequence analysis tool
2hFPG	2 h post-load plasma glucose
16S rRNA	16S ribosomal ribonucleic acid