Diet and microbiota in inflammatory bowel disease: The gut in disharmony

Table 1 Gut microbiota taxonomic classification and alterations associated with dietary patterns or the presence of inflammatory bowel disease

Phylum	Class	Order	Family	Genus	Species	Characteristics	Action in the GI tract	Ref.
Bacteroidetes	Bacteroidetes	Bacteroidales	Prevotellaceae	Prevotella	P. sp	Gram-negative	Diets rich in carbohydrates and fat	[10, 16, 22-24, 34, 35, 37, 38, 43, 44, 80, 82, 83]
				Bacteroides	B. fragilis	Anaerobic	Involved in colitis
					B. uniformis	Commensal bacteria
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium	C. lavalense	Gram-positive	Play a role in the clinical course of IBD	[10, 16, 21, 34, 37, 38, 43, 44, 80-84, 86, 87, 129, 159, 160, 181-185]
					C. perfringens	Anaerobic
			Ruminococcaceae	Ruminococcus	R. torques	Gram-positive	Fermentation of dietary fibre
						Anaerobic
				Faecalibacterium/ Fusobacterium	F. prausnitzii	Anaerobic Commensal bacteria
			Lachnospiraceae	Roseburia	R. faecis	Gram-positive	Fermentation of dietary fibre
					R. hominis	Anaerobic
					R. cecicola
					R. intestinalis
					R. inulinivorans
				Fusicatenibacter	F. saccharivorans		Present in the intestine
				Blautia	B. faecis
	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus	S. spp	Gram-positive	Part of the normal animal microbiota
			Lactobacillaceae	Lactobacillus	L. acidophilus		Induces remission in UC patients
	Negativicutes	Veillonellales	Veillonellaceae	Veillonella	V. spp	Gram-negative	Present in the intestine and oral mucosa
						Anaerobic
	Erysipelotrichia	Erysipelotrichales	Erysipelotrichaceae	Turicibacter	T. sp	Gram-positive	Present in mammal intestines
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Escherichia	E. coli	Gram-negative	Involved in colitis	[34, 36, 80, 83, 186]
		Desulfovibrionales	Desulfovibrionaceae	Bilophila	B. wadsworthia	Anaerobic
		Pasteurellales	Pasteurellaceae	Pasteurella	P. sp	Gram-negative	Present in the nose and mouth
						Commensal bacteria
						Facultative anaerobes
Actinobacteria	Actinobacteria	Bifidobacteriales	Bifidobacteriaceae	Bifidobacterium	B. breve	Gram-positive	Induces remission in UC patients	[159, 187]
					B. bifidum	Anaerobic
Fusobacteria	Fusobacteria	Fusobacteriales	Fusobacteriaceae	Fusobacterium	F. spp	Gram-negative	Involved in colitis and colon cancer	[83]
						Anaerobic

The five major bacterial phyla of the human GI microbiota and the potential relationship with diet and inflammatory bowel disease.