Table 1.

Summary of current microbiome-based therapeutic strategies in IBD.

Therapeutic	Examples	Effects on microbiome
Antibiotics	Rifaximin Ciprofloxacin Metronidazole Tobramycin Amoxicillin	➢ Eliminate specific microbial populations that contribute to hyperinflammatory states to modulate IBD severity/disease activity ➢ Prevent overgrowth of harmful microbial species that may lead to secondary IBD complications (e.g. pouchitis and abscesses) ➢ Influence the development of anti-drug antibodies that affect the risk of immunogenicity to anti-TNF biologics ➢ Increase risk of microbial resistance ➢ Increase risk of infections (e.g. Clostridium difficile)
Prebiotics (molecular compounds)	Lactulose Psyllium Fructo-oligosaccharides Germinated barley foodstuff	Metabolised by gut microorganisms to form small molecule by-products (e.g. butyrate and short-chain fatty acids) that influence the local microenvironment to preferentially favour growth of certain flora
Probiotics (living microorganisms)	Lactobacillus spp. Bifidobacterium spp. Saccharomyces spp. Non-pathogenic Escherichia coli	➢ Strengthen intestinal barrier function by inhibiting apoptosis of intestinal cells ➢ Regulate immunity through genetic pathways (NF-κB, IL-6, TNF-α) or direct influence on T-cells ➢ Produce small molecules (lactic acid, hydroperoxides) that directly influence the growth patterns of other microbial strains Provide local survival competition for scarce resources with other microorganisms
Synbiotics	Combination of prebiotics and probiotics	➢ Optimise a combination of prebiotics and probiotics for maximum synergistic effect ➢ Prebiotic(s) are specifically chosen to select for the growth and survival of probiotic organism(s)