NGS	Next-Generation Sequencing
GSMM	Genome-Scale Metabolic Modeling
HMP	Human Microbiome Project
SCFAs	Short-Chain Fatty Acids
BCFAs	Branched Chain Fatty Acids
BCAAs	Branched Chain Amino Acids
BAs	Bile Acids
TLR	Toll-Like Receptor
APCs	Antigen Presenting Cells
WGS	Whole Genomes Shotgun metagenomics sequencing
GEMs	Genome-Scale Models
T1D	Type 1 Diabetes
RA	Rheumatoid Arthritis
T2D	Type 2 Diabetes
NAFLD	Non-Alcoholic Fatty Liver Disease
IDB	Bowel Disease
CDS	Protein Coding Sequences
KEGG	Kyoto Encyclopedia of Genes and Genomes
HUMAnN2	HMP Unified Metabolic Analysis Network
MEGAN	MEtaGenome ANalyzer
MG-RAST	Metagenomics Rast
RAST	Rapid Annotation using Subsystem Technology
IMG/M	Integrated Microbial Genomes and Microbiomes
FBA	Flux Balance Analysis
CBA	Constraint-Based Approach
AGORA	Assembly of Gut Organisms through Reconstruction and Analysis
VMH	Virtual Metabolic Human
COBRA	COnstraint-Based Reconstruction and Analysis
RAVEN	Reconstruction, Analysis, and Visualization of Metabolic Networks
FVA	Flux Variability Analysis
SP	Shadow Price
UDCA	Ursodeoxycholate
RUTFs	Ready-to-Use Therapeutic Foods
EHMN	Edinburgh Human Metabolic Network
HMR	Human Metabolic Reaction
sIECs	small Intestinal Epithelial Cells
WBM	Whole-Body Metabolism
GF	Germ-Free
CONV-R	Conventionally Raised