| AHRQ | Agency for Healthcare Research and Quality |
| BCFA | branched-chain fatty acid |
| BMI | body mass index |
| CFU | colony-forming unit |
| COPD | chronic obstructive pulmonary disease |
| DIO | diet-induced obesity |
| DNA | deoxyribonucleic acid |
| DRI | dietary reference intake |
| DSHEA | Dietary Supplement Health and Education Act |
| EFSA | European Food Safety Authority |
| EPAS1 | endothelial PAS domain-containing protein 1 |
| EU | European Union |
| FAO | Food and Agriculture Organization |
| FD&C Act | Federal Food, Drug, and Cosmetic Act |
| FDA | U.S. Food and Drug Administration |
| 2’-FL | 2’-fucosyllactose |
| FMP | fermented milk product |
| FSDU | food for special dietary use |
| FSMA | Food Safety Modernization Act |
| FTC | Federal Trade Commission |
| GABA | gamma-aminobutyric acid |
| GalOS | galactooligosaccharide |
| GDP | gross domestic product |
| GI | gastrointestinal |
| GMO | genetically modified organism |
| GRAS | generally recognized as safe |
| GWAS | genome-wide association studies |
| HMO | human milk oligosaccharide |
| HMP | Human Microbiome Project |
| HUMAnN | HMP Unified Metabolic Analysis Network |
| IBD | imflammatory bowel disease |
| IBS | irritable bowel syndrome |
| ICU | intensive care unit |
| IFIC | International Food Information Council |
| IgA | immunoglobulin A |
| IHMC | International Human Microbiome Consortium |
| IL | interleukin |
| IND | Investigational New Drug |
| IOM | Institute of Medicine |
| IRB | institutional review board |
| ITC | isothiocynate |
| JCVI | J. Craig Venter Institute |
| LDL | low-density lipoprotein |
| LPS | lipopolysaccharide |
| LRH | liver receptor homologue |
| MAP | mitogen-activated protein |
| MDA | multiple displacement amplification |
| mRNA | messenger ribonucleic acid |
| MWAS | metabolome-wide association studies |
| NDI | new dietary ingredient |
| NDO | nondigestible oligosaccharide |
| NEC | necrotizing enterocolitis |
| NIH | National Institutes of Health |
| NMR | nuclear magnetic resonance |
| NSF | National Science Foundation |
| OTU | operational taxonomic unit |
| PCR | polymerase chain reaction |
| PDX | polydextrose |
| PKU | phenylketonuria |
| qRT | quantitative real-time |
| rDNA | ribosomal deoxyribonucleic acid |
| rRNA | ribosomal ribonucleic acid |
| RYGB | Roux-en-Y gastric bypass |
| SCF | soluble corn fiber |
| SCFA | short-chain fatty acid |
| TF | transcription factor |
| TJP1 | tight junction protein 1 |
| TLR | Toll-like receptor |
| TNBS | 2,4,6-trinitrobenzenesulfonic acid |
| TNF | tumor necrosis factor |
| USDA | U.S. Department of Agriculture |
| WHO | World Health Organization |