Table 3.
Potential gene/protein markers related to different probiotic properties identified during genetic and omics studies.
| Gene/protein | Function | Representative references |
|---|---|---|
| Stress responses (acid and bile) | ||
| Heat shock proteins (e.g., DnaK, GroES, GroEL, GrpE) | Repair of damaged proteins | Wu et al. (2010), Ruiz et al. (2012), Hamon et al. (2014) |
| Clp proteases (e.g., ClpP, ClpE, ClpL) | Refolding or degrading denatured proteins | Ferreira et al. (2013), Hamon et al. (2014) |
| uvrB, uvrD1, vsr, helicases | DNA repair | Jin et al. (2012), An et al. (2014) |
| F1F0-ATPase | Decrease of intracellular pH | Sanchez et al. (2008), Hamon et al. (2011), Jin et al. (2012), Koponen et al. (2012) |
| manB, glmU, dapA, glycosyltransferases | Peptidoglycan biosynthesis | Jin et al. (2012) |
| dlt operon | D-alanylation of lipoteichoic acids | Perea Velez et al. (2007), Koskenniemi et al. (2011) |
| fab genes | Fatty acid biosynthesis | Koponen et al. (2012), An et al. (2014) |
| Etk-like tyrosine kinase, welG | Exopolysaccharide biosynthesis | Koskenniemi et al. (2011), Jin et al. (2012) |
| FabF, RfbB, RfbC | Cell envelope biogenesis | Hamon et al. (2014) |
| luxS | Cell-to-cell communication | Moslehi-Jenabian et al. (2009), Wu et al. (2010), Koponen et al. (2012) |
| bsh | Deconjugation of bile salts | Hamon et al. (2011), Koskenniemi et al. (2011), An et al. (2014) |
| Transporters | Bile efflux | Price et al. (2006), Gueimonde et al. (2009), Koskenniemi et al. (2011), Ruiz et al. (2012), An et al. (2014) |
| Adhesion | ||
| Mub | Cell-surface proteins with cell wall anchoring motif (LPXTG) | Azcarate-Peril et al. (2008), Mackenzie et al. (2010), Weiss and Jespersen (2010), Turpin et al. (2012) |
| slpA | S-layer protein | Falentin et al. (2010), Ashida et al. (2011), Beganovic et al. (2011), Turpin et al. (2012) |
| Apf | Aggregation promoting factor | Ventura et al. (2002), Turpin et al. (2012) |
| srtA | Sortase-dependent surface protein | Munoz-Provencio et al. (2012) |
| spaCBA, spaFED, pil2, pil3, fim1, fim2, fim3 | Sortase-dependent biosynthesis of pili | Kankainen et al. (2009), Foroni et al. (2011), Gilad et al. (2011), Westermann et al. (2012), Douillard et al. (2013), Turroni et al. (2013) |
| FbpA, E1 β-subunit of the pyruvate dehydrogenase complex | Fibronectin binding protein | Azcarate-Peril et al. (2008), Weiss and Jespersen (2010), Vastano et al. (2014) |
| tad | Assembly of tide adherence pilus | Westermann et al. (2012) |
| Degradation of HMOs and Mucus | ||
| 43 kbp gene cluster | Catabolism of HMOs | Sela et al. (2008) |
| F1SBPs | Import of oligosaccharides | Sela et al. (2008) |
| β-Galactosidases | Degradations of type-1 and type-2 HMOs | Yoshida et al. (2012) |
| Glycosylases | Degradation of HMOs | Kim et al. (2009) |
| Glycosyl hydrolases, exo-α-sialidases, fucosidases, PTS systems, ABC-type carriers, specific permeases, engBF, afcA, NagBb, AgnB | Mucin degradation | Yang et al. (2007), Ruas-Madiedo et al. (2008), Turroni et al. (2010a, 2011), Kiyohara et al. (2012), Shimada et al. (2014) |
| adh | Adhesion and stimulation of mucin secretion | Mack et al. (2003) |
| Soluble protein p40 | Stimulation of mucin production | Wang et al. (2014) |
| Modulation of the immune system | ||
| p40 and p75 proteins and homologues | Activation Akt, promotion of cell growth, inhibition of TNF-α | Yan et al. (2007), Bauerl et al. (2010) |
| ClpB, Rpf | Potential immunogenic proteins | Gilad et al. (2011) |
| SLPs (SlpA, InlA, LspA, SlpE, SlpB), additional disperse genetic loci | Regulation of anti- or pro-inflammatory immune responses (e.g., induction of the IL-10 and IL-6 regulatory cytokines) | Konstantinov et al. (2008), Meijerink et al. (2010), van Hemert et al. (2010), Beganovic et al. (2011), Le Marechal et al. (2014) |
| ser | Inhibition of elastases | Turroni et al. (2010b) |
| Cell surface-associated EPS | Adaptive immune response and protection against the gut pathogen Citrobacter rodentium | Fanning et al. (2012) |
| Flagellin | Induction of human β-defensin 2 (hBD-2) | Schlee et al. (2007) |
| Production of antimicrobial compounds | ||
| Bacteriocins | Protection against enteropathogens | Corr et al. (2007) |
| Genes involved in plantaricin biosynthesis and secretion | Regulation of pro- and anti-inflammatory cytokines of DCs | Meijerink et al. (2010) |
| Quorum sensing | ||
| luxS | Induction of anti-inflammatory cytokines Adhesion and competitive exclusion of pathogens | Jacobi et al. (2012) Buck et al. (2009), Moslehi-Jenabian et al. (2011) |
| lamBDCA operon, lamKR operon | agr-like quorum sensing systems | Sturme et al. (2005), Fujii et al. (2008) |
| Quorum sensing system related peptide (CHWPR) | Induction of c-myc and IL-6 genes in somatic cells | Mitsuma et al. (2008) |
| Production of nutrients and other beneficial processes | ||
| Vitamins, essential amino acids, SCFAs | In situ production of important nutrients | Falentin et al. (2010), Saulnier et al. (2011) |
| fos | Processing of health-promoting fructooligosaccharides | Ryan et al. (2005), Kim et al. (2009) |
| ABC carbohydrate transporters | High production of acetate and protection from enteropathogenic infection | Fukuda et al. (2012) |
| ccpA | Influencing blood cholesterol | Lee et al. (2010) |