Table 1.

Association between the gut microbiome and inflammatory bowel disease.

Microbiome Components	Presence in IBD	Possible Mechanisms	Evidence	References
Firmicutes
Faecalibacterium prausnitzii		It is a highly active metabolic commensal bacterium involved in the production of butyrate. This metabolite plays a major role in gut physiology and has beneficial effects, including protection against pathogen invasion, modulation of the immune system, and promotion of anti-inflammatory activity	Presence of F. prausnitzii may serve as a biomarker of intestinal health in adults. Low levels of this bacteria could be predictive for CD. Its deficiency was shown in colonic CD. Low F. prausnitzii levels in patients with IBD undergoing surgery is associated with a higher risk of post-operative recurrence	[25,27]
Eubacterium spp.		Involved in the production of SCFAs, especially butyrate. It is important in inflammation modulation and the promotion of epithelial barrier integrity	Found deficient in samples from patients with CD and UC	[24,28]
Ruminococcus albus		Possibly involved in SCFA metabolism and its protective and anti-inflammatory roles	Found decreased in samples from patients with CD and UC	[24,29]
Ruminococcus gnavus		Involved in bile and amino acid biosynthesis pathways, including amino acid, energy, carbohydrate, and nucleotide metabolism Lack of supporting evidence of possible mechanisms involved	Found decreased in the stool of patients with treatment-naïve new-onset CD Found increased in samples from patients with CD compared to controls	[24,30]
Clostridioides difficile		A and B toxins produced by this bacterium may activate caspase-1 and secrete mature IL-1b and IL-18 (proinflammatory cytokines) that cause damage to the epithelial barrier and intestinal cells	High prevalence of infection by C. difficile has been demonstrated among patients with IBD	[31,32]
Listeria monocytogenes		Possibly associated with invasive infection of epithelial cells	Listeria monocytogenes infection rates seem to be elevated in patients with IBD	[31,33]
Verrucomicrobia
Akkermansia muciniphila		Possibly involved with the production of SCFAs, which can activate the GPR43 and thereby increase the number of Foxp3+ regulatory T cells in the colon	Decreased in stools of both CD and UC patients. Human strain ATCC BAA-835T and murine strain 139 exerted anti-inflammatory effects on DSS-induced chronic colitis in mice	[34,35,36]
Actinobacteria
Eggerthella lenta		Lack of well-explored possible mechanisms	Found increased in samples from patients with CD compared to controls	[24]
Bifidobacterium bifidum		Mucin metabolism performed by B. bifidum could activate enhanced production of mucin, thereby increasing the mucus layer depth and strengthening the epithelial barrier function	Found decreased in samples from patients with IBD. Some studies suggest that probiotics containing this bacterium could have positive responses in the treatment of IBD	[37,38]
Mycobacterium avium		Associated with increased production of proinflammatory cytokines. Mutations in NOD2/CARD15 receptors may cause intracellular survival of the bacteria and ultimately cause infection	The abundance of this bacteria, especially the subspecies paratuberculosis, is higher in patients with IBD than in controls	[39,40]
Proteobacteria
Escherichia coli		Epithelium-associated invasive E. coli has frequently been isolated from ileal and colonic mucosa from patients with CD and can infect and damage intestinal epithelial cell monolayers, and synthesize α-hemolysin	Found increased numbers of E. coli strains with virulence properties isolated from samples of patients with IBD. Several studies indicate that there is a link between the prevalence of E. coli and IBD relapses	[41,42]
Haemophilus parainfluenzae		Involved in glycerol-phospholipid and lipopolysaccharide metabolism, thereby promoting inflammation	Found increased in stool samples from patients with treatment-naïve new-onset CD	[30]
Campylobacter spp.		Invasive strains of this bacteria in patients with IBD can survive in intracellular and anaerobic conditions	Increased in patients with IBD compared to controls	[43]
Eikenella corrodens		Possibly involved in lipid and polysaccharide metabolism, resulting in proinflammatory responses	Increased in patients with IBD compared to controls	[30]
Fusobacteria
Fusobacterium nucleatum		Possibly involved in proinflammatory and tumorigenic responses	Increased in patients with IBD compared to controls. It is also associated with colorectal cancer	[43]
Bacteroidetes
Bacteroides spp.		Involved in mucin metabolism, possibly playing a role in damaging the protective mucus layer	Increased in CD samples. Prominent in patients with prior surgical resection	[24,44,45,46]

Abbreviations: CD, Crohn’s disease; G protein-coupled receptor 43 (GPR43); IBD, inflammatory bowel disease; SCFAs, short-chain fatty acids; UC, ulcerative colitis; IL, interleukin; NOD2/CARD15, nucleotide-binding oligomerization domain 2/caspase recruitment domain family, member 15.