|AIDS||acquired immune deficiency syndrome|
|AMD||acid mine drainage|
|BAM||bacteriophage adherence to mucus|
|CA-MRSA||community-acquired methicillin-resistant S. aureus|
|CBER||Center for Biologics Evaluation and Research|
|CDC||U.S. Centers for Disease Control and Prevention|
|DOE||U.S. Department of Energy|
|FDA||U.S. Food and Drug Administration|
|FMT||fecal microbiota transplantation|
|HIV||human immunodeficiency virus|
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Appendix C Acronyms AIDS acquired immune deficiency syndrome AMD acid mine drainage AMP antimicrobial peptide ATP adenosine triphosphate BAM bacteriophage adherence to mucus CA-MRSA community-acquired methicillin-resistant S. aureus CBER Center for Biologics Evaluation and Research CD Crohn’s disease CDC U.S. Centers for Disease Control and Prevention DOE U.S. Department of Energy DIO diet-induced obesity DNA deoxyribonucleic acid FDA U.S. Food and Drug Administration FMT fecal microbiota transplantation GE gastroesophageal GEJ gastroesophageal junction GI gastrointestinal GIO gene-induced obesity HIV human immunodeficiency virus 501
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502 MICROBIAL ECOLOGY IN STATES OF HEALTH AND DISEASE HMO human milk oligosaccharides HMP Human Microbiome Project IBD inflammatory bowel disease iNKT invariant natural killer T IOM Institute of Medicine MAMP microbe-associated molecular pattern MIO microbe-induced obesity mRNA messenger ribonucleic acid MRSA methicillin-resistant S. aureus NASH nonalcoholic steatohepatitis NIAID National Institute of Allergy and Infectious Diseases NIH National Institutes of Health NO nitric oxide NSF National Science Foundation OPC oropharyngeal candidiasis OTU operational taxonomic unit PAMP pathogen-associated molecular pattern PAT pulsed antibiotic treatment PCoA principal coordinate analysis PCR polymerase chain reaction POP pattern of pathogenesis PRR pattern-recognition receptor rDNA ribosomal deoxyribonucleic acid RNA ribonucleic acid rRNA ribosomal ribonucleic acid RYGB Roux-en-Y gastric bypass SCFA short-chain fatty acid SIV simian immunodeficiency virus STAT subtherapeutic antibiotic treatment TMAO trimethylamine N-oxide VVC vulvovaginal candidiasis