Probiotics, their action modality and the use of multi-omics in metamorphosis of commensal microbiota into target-based probiotics

Abstract

This review article addresses the strategic formulation of human probiotics and allows the reader to walk along the journey that metamorphoses commensal microbiota into target-based probiotics. It recapitulates what are probiotics, their history, and the main mechanisms through which probiotics exert beneficial effects on the host. It articulates how a given probiotic preparation could not be all-encompassing and how each probiotic strain has its unique repertoire of functional genes. It answers what criteria should be met to formulate probiotics intended for human use, and why certain probiotics meet ill-fate in pre-clinical and clinical trials? It communicates the reasons that taint the reputation of probiotics and cause discord between the industry, medical and scientific communities. It revisits the notion of host-adapted strains carrying niche-specific genetic modifications. Lastly, this paper emphasizes the strategic development of target-based probiotics using host-adapted microbial isolates with known molecular effectors that would serve as better candidates for bioprophylactic and biotherapeutic interventions in disease-susceptible individuals.

Keywords: bioprophylactics; biotherapeutics; host-adapted strains; human probiotics formulation; lactic acid bacteria; multi-omics; target-based probiotics.

FIGURE 1

A brief history of probiotics. CBER, Center for Biologics Evaluation and Research; EFSA, European Food Safety Authority; FAO, Food and Agriculture Organization; FDA, Food and Drug Administration; ISAPP, International Scientific Association for Probiotics and Prebiotics; WHO, World Health Organization. The figure was drawn with BioRender.

FIGURE 2

Probiotics action modality. Probiotics employ various mechanisms to exert their beneficial effects on the host including: (1) probiotics compete pathobionts and pathogens for microbial resources needed for growth and metabolism, e.g., acquisition of monosaccharides; (2) probiotics inhibit pathogens by producing antimicrobials, e.g., SCFAs, bacteriocins, antibiotics, microcins, etc.; (3) probiotics metabolize substrates into useful products, e.g., organic acids and volatile fatty acids; (4) probiotics produce growth substrates for beneficial microbiota and the host, e.g., folate and riboflavin; (5) probiotics induce immunomodulatory responses either by direct contact or surface molecules like SpaCBA, SD-pili, LTA, and sEPS; immune stimulation favors elevated expression of IgA and SCFAs in pathogenic infections and decreased expression of IgE and IgG in allegro-inflammatory responses via stimulating DCs, TLRs, NK cells, and lymphocytes; (6) sEPS facilitate probiotics to auto-aggregate and form protective biofilms and, co-aggregate with pathogens to prevent them from colonizing the host epithelial surfaces; (7) probiotics maintain barrier integrity by regulating TJ proteins (claudin-1, occludin, ZO-1) and by mucus formation via elevated expression of MUC 1,2,3 and 5a; Slps facilitate attachment of the probiotic strains to the gut epithelium; the colonization of pathogens is inhibited through pathogen displacement; (8) probiotics reduce inflammation by upregulating anti-inflammatory and downregulating pro-inflammatory mediators; CXCR3, C-X-C Motif Chemokine Receptor 3; BLIS, bacteriocin-like inhibitory substances; DC, dendritic cell; FOXP3, forkhead box p3; H₂O₂, hydrogen peroxide; IFN-γ, interferon-gamma; Ig, immunoglobulin; IL, interleukin; LTA, lipoteichoic acid; MUC, Mucin; NF-κB, nuclear factor-kappa light chain enhancer of activated B cells; NK, natural killer; SCFA, short chain fatty acids; SD-pili, sortase-dependent pili; sEPS, surface exopolysaccharides; Slps, surface-layer proteins; spaCBA, heterotrimeric pili complex made of protein subunits spa C, spa B and spa A; TEER, trans-epithelial electrical resistance; TGF-β, transforming growth factor-beta; Th, T-helper; TJ, tight junction; TLR, toll-like receptor, TNF-α, Tumor necrosis factor-alpha; Treg, T regulatory. The figure was drawn with BioRender.

FIGURE 3

Venn diagram of factors affecting the efficacy of probiotics. The efficacy of a probiotic is a result of the interplay between numerous strain-specific and host-specific factors. The figure was drawn with BioRender.

FIGURE 4

Limitations of non-human lineage strains as probiotics. The probiotic formulations based on non-human associated strain often fail to produce health-promoting effects in clinical trials possibly because they did not co-evolve with their respective host and consequently do not carry niche-specific genetic modifications. The figure was drawn with BioRender.

FIGURE 5

Host-adapted strains harbor niche-specific phenotypic fitness. The host-adapted microbial strains carry niche-specific genetic signatures which enable them to adapt to the host ecosystems efficiently. These genetic modifications enable higher metabolic activity (larger carbohydrate utilization cassettes, production of β-galactosidases, etc.), higher resistance to enteropathogens (production of lactic acids, synthesis of secondary metabolites, etc.), higher immune tolerance (induction of anti-inflammatory cytokines like IL-10, IL-13, etc.), and higher functional profiles (production of bile salt hydrolases to endure bile salts, accumulation of ATP synthesizing cassettes for conditional respiration, etc.). Thus, host-adapted microbial strains possess a large repertoire of niche-specific genes that facilitate their persistence in the host. The figure was drawn with BioRender.

FIGURE 6

The formulation of target-based probiotics. The formulation of target-based probiotics is based on understanding the action modality of probiotic strains via a multi-omics approach and then tailoring a probiotic formulation that produces molecular effectors to ameliorate a specific disease or indication; IECs, intestinal epithelial cells. The figure was drawn with BioRender.