The infant gut microbiome in early life is shaped by numerous factors, including feeding method. Exclusively breastfed and formula-fed infants exhibit distinct microbiome compositions. While these effects are well-established, the underlying mechanisms that drive these differences are not fully understood. Here, we examine the removal of sialic acid from human milk oligosaccharides (HMOs) influenced by human microbial sialidases in early life. We identify 351 and 214 unique sialidase sequences from adult and infant microbiome metagenomes, respectively, and characterize a diverse, representative set in vitro using sialylated HMOs normally present in human breastmilk. We find these proteins exhibit distinct abilities to metabolize 3’- and 6’-sialyllactose, which are the most abundant sialylated HMOs in breastmilk, and distinctly process other more complex substrates, as well. We provide structural insights into these functional differences by pinpointing active site features uniquely present in efficient enzymes and show that these results extend to activities on complex mixtures of sialylated HMOs purified from human breastmilk. Finally, we demonstrate in human clinical data that distinct profiles of sialidase-encoding bacterial taxa are observed in breastfed and formula-fed infants at 1 and 4 months of age, prior to the introduction of solid foods. Together, these findings show that specific bacterial sialidases are influential in shaping the early gut microbiome, data that may improve the supplementation of infant formulas for enhanced developmental outcomes.
The gut microbiota is increasingly recognized as a systemic regulator of host immunity, host metabolism, epithelial barrier integrity, and distal tissue homeostasis. Hematologic disorders provide an important setting in which these host–microbe interactions converge on immune remodeling, marrow-niche function, hematopoietic recovery, treatment response, and transplant-related complications. This narrative review synthesizes mechanistic, clinical, and translational evidence linking gut microbial dysbiosis to benign and malignant hematologic diseases, clonal and premalignant states, and hematopoietic stem cell transplantation (HSCT)-related outcomes. Rather than treating microbiome associations as a single evidence category, we distinguish five complementary evidence strata: Mendelian randomization, experimental models, prospective human cohorts, randomized human interventions, and cross-sectional studies. These study designs address different causal questions and are interpreted as complementary rather than as a single linear hierarchy. We also separate microbial composition from microbial function: taxon-level enrichment or depletion is treated primarily as context-dependent and hypothesis-generating, whereas conserved functional pathways—including short-chain fatty acids, bile-acid transformation, tryptophan metabolism, microbial translocation and barrier dysfunction, and innate immune activation—provide the principal cross-disease mechanistic framework. We integrate disease-specific microbial features, functional mediators, immune and marrow consequences, and clinical outcomes into an author-constructed evidence map, while explicitly addressing bidirectionality, reverse causality, and translational readiness. Emerging applications include microbiota-based biomarkers, treatment-response prediction, fecal microbiota transplantation, probiotics and postbiotics, antibiotic stewardship, and microbiota-dependent modulation of drug metabolism.
Fecal microbiota transplantation (FMT) modifies gut bacterial composition and improves metabolic outcomes in subjects with obesity and type 2 diabetes (ObT2), but bacterial changes alone do not fully explain the heterogeneity in clinical response. We performed virus-like particle (VLP)-enriched metagenomic sequencing coupled with bulk-DNA metagenomic sequencing on longitudinal fecal samples from a randomized controlled FMT trial in ObT2. Using random forest classification, post-FMT virome changes showed accuracy comparable to bacteriome changes (84.8% vs 81.4%) in distinguishing LDL responders from non-responders. Donor-derived viral contig engraftment was detected in 64.7% (11/17) of recipients receiving FMT alone and 58.8% (10/17) receiving FMT with lifestyle intervention (LSI), versus 5.6% (1/18) in the sham with LSI group. FMT was associated with increased virome diversity, compositional shifts toward the donor virome, and coordinated virus–bacteria associations, with most responsive viral contigs classified as Caudoviricetes. FMT-responsive viral contigs that were shared between the two FMT groups were predicted to infect Roseburia and Bifidobacterium, while contigs associated with clinical responses were predicted to infect Escherichia, Roseburia, Blautia, and Enterococcus. These findings suggest that the gut virome is a complementary ecological component associated with FMT responses and metabolic outcomes in ObT2.
Necrotizing enterocolitis (NEC) remains a major cause of gastrointestinal morbidity and mortality in preterm infants, with no targeted mechanism-based therapy. Aryl hydrocarbon receptor (AhR) signaling is an emerging host–microbe interface because it integrates dietary, microbial, milk-derived, and host-derived ligands that regulate intestinal inflammation, epithelial homeostasis, and barrier integrity. Direct NEC-specific evidence for individual AhR ligands, however, remains sparse and uneven. This focused review maps direct NEC intervention evidence, independent replication, human NEC association or ex vivo evidence, AhR dependency, compartment specificity, mechanistic resolution, and translational considerations. Indole-3-carbinol (I3C), the synthetic agonist A18, and 3-indoleacrylic acid (IA) have direct intervention evidence in experimental NEC models. Two independent NEC studies support I3C, although the implicated cellular compartment differs between models. A18 provides direct protection in an experimental NEC model, activates AhR, and exhibits anti-inflammatory effects in human intestinal explants. However, it has not been independently replicated. IA is currently the most comprehensively characterized microbiota-derived ligand in NEC models. However, its mechanistic evidence predominantly comes from one recent study and awaits independent replication. Indole-3-lactic acid, indole-3-acetic acid, and indole-3-sulfate remain physiologically relevant candidates, supported by immature intestinal, human milk, or neonatal metabolic studies. Overall, current evidence supports a ligand-specific view of AhR biology in NEC while highlighting major gaps in replication, human validation, and translational studies.
Host–microbe interactions are essential for maintaining intestinal homeostasis, yet most in vitro models lack physiological oxygen gradients, mucosal architecture, and reproducibility. We developed the Mucosal Mimetic 3D–Host Aerobic Microbiota Anaerobic Co-culture (Mm 3D-HaeMan) system, a colon-mimetic, oxygen-stratified platform enabling stable co-culture of colonic epithelial cells, human peripheral blood mononuclear cells (hPBMCs), and obligate anaerobes. Oxygen profiling confirmed a stable gradient consistent with human colonic stratification. Using a canonical short-chain fatty acid (SCFA) cross-feeding pair (Anaerostipes caccae and Bifidobacterium bifidum, AcBb consortium), we performed integrated, multilayered analyzes of the host-microbe interface. Co-culture with the SCFA-producing AcBb consortium was associated with enhanced epithelial-mitochondrial respiration, maintenance of transepithelial resistance, tight junction protein expression without barrier disruption, and rebalanced cytokine profiles. Host transcriptomics identified 41 differentially expressed genes (15 upregulated, 26 downregulated) associated with homeostatic-relevant epithelial responses. Simultaneously, bacterial metatranscriptomics revealed 29 differentially expressed gene families; notably, glaK was enriched in bacteria-only cultures; SORD, nuoG, and nuoE were specifically induced during co-culture, indicating host-associated bacterial transcriptional changes. The compartmentalized design permits independent sampling for layer-resolved multi-omics and functional readouts. These findings establish Mm 3D-HaeMan as a physiologically grounded platform for dissecting bidirectional host–microbe responses and immune-associated interactions. This model offers broad applicability for mechanistic research and translational screening of probiotics and microbiome-based therapeutics.
