Table 3 Taxa detected in SC2 taxonomic consensus signature and k-mer-based signature connected to IBD through the literature review. Taxonomy levels are marked as: Class (C), Order (O), Family (F), Genus (G), Species (S), Strain (STR).

FIRMICUTES, Clostridia order

 G: Roseburia, Ruminococcus, Eubacterium, Faecalibacterium

k-mer & SC2

Short Chain Fatty Acids (SFCA) production¹⁷

 S: R. hominis, A. hardus

k-mer & SC2

Butyrate production^18,19,20

 F: Eubacteriaceae

 S: F. prausnitzii

k-mer &SC2

Butyrate and anti-inflammatory cytokine production, suppression of pro-inflammatory cytokines¹⁸

 S: C. difficile

k-mer

IBD-induced (due to bile acids inhibition) growth causing IBD symptoms and complications^21,22

FIRMICUTES, Lactobacillales order

 Order in general

k-mer

IBD-associated relative abundance change²³

 S: L. gazeri

k-mer

Improves colitis symptoms in mice²⁴

 S: L. rhamnosus, E. faecium, L. plantarum, L. acidophilus

k-mer

Multi-strain probiotic associated with decreased inflammation in patients with UC, but not in CD²⁵

PROTEOBACTERIA

 G: Klebsiella, Salmonella

 S: E. coli

k-mer & SC2

Pro-inflammatory and colitogenic pathobionts^26,27,28,29

 G: Pseudomonas

SC2

Pro-inflammation (epithelial cell damage) agent³⁰

 G: Campylobacter

SC2

Pro-inflammatory cytokines production³¹

 STR: cytogenic strains of Class Alphaproteobacteria

SC2

Antagonizing Lachnospiraceae family, thus increasing IBD symptoms³²

 C: Bettaproteobacteria

k-mer

IBD-associated relative abundance change³³

BACTEROIDETES

 O: Flavobacteriales, Cytophagales

SC2

Decreased abundance is associated with IBD status. Through the sphingolipids production influences the severity of intestinal inflammation and alters host ceramide pools^34,35,36,37

 O: Bacteroidales

k-mer

 S: B. fragilis, B. vulgatus

k-mer

Attenuates pathogenic bacteria-induced colitis^38,39

 STR: B. fragilis (enterotoxigenic strains)

k-mer

Increases inflammation by producing certain toxins and pro-inflammatory cytokines⁴⁰

 S: B. longum

k-mer

Immune responses induction and regulation; inflammatory cytokines expression reduction⁴¹

 S: B. adolescentis

k-mer

Folate productions (reduces the inflammation)⁴²

 Coriobacteriaceae

Lactate, formate, acetate, and hydrogen sulfate metabolism regulation^43,44,45

 Eggerthellaceae

IBD-associated relative abundance change⁴⁶

FUSOBACTERIUM

 S: F. nucleatum

k-mer

Promotion of proinflammatory cytokine secretion and thus damaging the intestinal barrier⁴⁷

CYANOBACTERIA

SC2

IBD-associated relative abundance change⁴⁸

VERRUCOMICROBIA

 G: Akkermansia Verrucomicrobium

SC2

SCFA-producing, decreased relative abundance in IBD subjects^49,50

 S: A. muciniphilia

SC2

Colonic mucus restoration⁵⁰