Aim: This study investigated the effects of Muno-IgY®, a multi-pathogen-specific immunoglobulin Y (IgY), on microbial growth, adhesion, fermentation activity, and immune signaling using a multi-tiered in vitro approach.

Methods: IgY activity was first evaluated in Caco-2 adhesion and invasion assays using adherent-invasive Escherichia coli (AIEC) at optimized concentrations, followed by assessment in a SHIME® in vitro gut model inoculated with human fecal microbiota enriched in Enterobacteriaceae. Microbial composition, fermentation markers, and metabolite production were analyzed, and downstream effects on epithelial barrier integrity and immune signaling were evaluated using a Caco-2/peripheral blood mononuclear cell (PBMC) co-culture model exposed to SHIME® effluents.

Results: Muno-IgY® significantly reduced AIEC adhesion/invasion from 39.76% in controls to 13.08% and 9.13% at 3 and 6 mg/mL, respectively (P < 0.05). In the SHIME® model, IgY significantly increased acetate and propionate production (P < 0.05), alongside a marked increase in ammonium concentration (P < 0.01). Microbial biomass increased modestly, while alpha- and beta-diversity indices were not significantly altered. The compositional shifts indicated enrichment of beneficial and mucin-associated taxa and reduction of opportunistic or pathogenic species in the Muno-IgY® group. In Caco-2/PBMC co-cultures, IgY-treated effluent decreased transepithelial electrical resistance (TEER) indicating reduced barrier integrity (P < 0.05) but significantly decreased pro-inflammatory cytokines Interferon-γ (IFN-γ) and Interleukin-22 (IL-22) (P < 0.05).

Conclusions: Muno-IgY® demonstrates the ability to inhibit pathogen adhesion and modulate microbial composition and immune responses in vitro. These findings support its potential as a non-antibiotic approach for microbiome-targeted interventions, although further validation in vivo is required.

Background:Klebsiella pneumoniae can colonize the gastrointestinal tract, yet its interactions with intestinal mucus remain poorly defined. In this study, we examined the capacity of Klebsiella pneumoniae (K. pneumoniae) to adhere and use intestinal mucus and its associated glycans.

Methods: Multiple commercial and clinical K. pneumoniae isolates were tested for adhesion to porcine and human Mucin 2 (MUC2) using fluorescence-based assays and microscopy. In vivo mucus localization was examined in colonized mice by fluorescent in situ hybridization (FISH). Genomic analyses of K. pneumoniae genomes were performed to identify glycosyl hydrolases and sugar utilization pathways. Growth on mucin-derived monosaccharides or intact mucus was assessed in minimal media. Biofilm formation and aminoglycoside susceptibility were measured in the presence or absence of mucus.

Results: All K. pneumoniae strains adhered robustly to porcine and human MUC2 in vitro and we found K. pneumoniae localized to the murine mucus layer in vivo. Genomic analysis of over 1,000 K. pneumoniae isolates revealed that most strains possess glycosyl hydrolases targeting internal galactose, N-acetyl-glucosamine (GlcNAc), and N-acetyl-galactosamine (GalNAc) glycan sugars, though they lack enzymes to cleave terminal fucose or N-acetyl-neuraminic acid. Consistent with this finding, we found that K. pneumoniae alone could not grow in minimal media with intact mucus as a sole carbon source. However, we found that K. pneumoniae could grow with free mucus glycan-derived sugars galactose, GlcNAc, GalNAc fucose and N-acetyl-neuraminic acid. Mucus did not alter biofilm formation, but it significantly increased sensitivity to gentamicin, kanamycin and streptomycin.

Conclusion: These findings identify mucus as an important modulator of K. pneumoniae colonization and antibiotic responsiveness.

The gut virome, comprising bacteriophages and eukaryotic viruses, represents a complex and dynamic component of the intestinal microbiome whose functional significance has long been underestimated. Emerging evidence highlights the gut virome as a pivotal modulator of the host immune system, particularly in regulating the balance and function of regulatory T cells (Tregs), which are essential for maintaining immune homeostasis. This review distinguishes two mechanistic axes by which the virome influences Tregs: (i) an indirect ‘virome-bacteriome-metabolite-Treg axis’, and (ii) a direct ‘viral pathogen-associated molecular patterns (PAMPs)-pattern recognition receptors (PRRs)-Treg’ signaling axis. This review comprehensively examines the dualistic role of the gut virome in preserving intestinal equilibrium and its involvement in the pathogenesis or amelioration of intestinal inflammatory disorders such as inflammatory bowel disease (IBD). Furthermore, the influence of the gut virome extends beyond the gut, potentially impacting systemic immune-related diseases. By integrating recent advances in metagenomics, viromics, and immunology, we elucidate the molecular mechanisms through which the gut virome orchestrates immune regulation. This synthesis aims to provide a comprehensive understanding of the gut virome as a critical immune regulator and to explore its potential as a biomarker for disease diagnosis and a novel target for therapeutic intervention.

The early-life gut microbiome is tightly linked to different aspects of infant development. Microbial colonisation patterns have been repeatedly shown to play a role in a variety of paediatric outcomes, ranging from metabolism and immune function to neurodevelopment. Concomitantly, the identification of early-life biomarkers is crucial, especially considering that for various conditions, reliable diagnostic tools only emerge in early childhood. As such, microbiome data collected in the first two years of life may offer valuable prospects for early detection, prevention, quantification or even correction of adverse health trajectories. With the increasing availability of high-resolution microbiome data, researchers are leveraging both traditional statistical approaches and machine learning (ML) methods to analyse the evolution of these complex microbial communities. While statistical models are well-suited for identifying associations between microbiome features and health states, ML methods allow for predicting health outcomes from those features. This review explores the role of the early-life gut microbiome in infant health and development, with a focus on how data acquisition and analytical methods can shape current knowledge. We contrast statistical approaches with ML methods, summarising key findings on microbial succession and factors influencing it. By addressing current challenges and identifying areas for methodological refinement, we aim to discuss the potential of the microbiome in the assessment of current and future health states of an individual and aid in the development of more robust, clinically-relevant models for paediatric care.