Unveiling the viral dimension: The paediatric gut virome as a key modulator of gastrointestinal metabolic, and neurodevelopmental health

Table 1 Comparative landscape of the human gut bacteriome and virome

Metric	Gut bacteriome	Gut virome
Numerical abundance	1011-1012 cells per gram of feces	109-1012 particles per gram of feces (VLPs)1
Biomass contribution	Major (99.9% microbial biomass)	Minimal (< 0.1% of microbial biomass)
Universal genetic marker	Present (16S rRNA gene)	None (Requires shotgun metagenomics)
Database maturity	High (most sequences are identifiable)	Low (40%-90% “viral dark matter”)2
Identification logic	Taxonomy-based (16S) or functional	Homology-based or de novo assembly
Major constituents	Bacteria, archaea	Bacteriophages, eukaryotic viruses, archaeal viruses, and EVEs
Replication strategy	Predominantly binary fission	Lytic, lysogenic (prophages), and chronic
Pediatric trajectory	Diversity increases linearly with age	Richness often peaks in infancy and fluctuates
Study cost/complexity	Lower (standardized and high-throughput)	Higher (requires enrichment and heavy compute)

¹Numerical Paradox: While viruses often outnumber bacteria in particle count, their lack of biomass made them “invisible” to early bulk sequencing methods.

²Viral dark matter: Refers to sequences that do not align with any known reference in public databases.

EVEs: Endogenous viral elements; VLP: Virus-like particles.

Table 2 Determinants of the developing paediatric gut virome

Factor	Primary impact on virome composition	Age-dependent outcome
Mode of delivery	Vaginal: Vertical seeding of maternal phages (e.g., Caudoviricetes). C-section: Initial colonization by skin-associated and environmental viruses	VD: Earlier stabilization of the bacteriome-phage axis. CS: Delayed maturation and reduced alpha-diversity up to 24 months
Infant diet	Breast milk: Direct transfer of TTV/CMV; HMOs act as “decoy receptors” for pathogens. Formula: Distinct eukaryotic signature; lacks maternal immune factors	Breastfed: Sustained “healthy” phage-host dynamics; lower risk of early-life viral gastroenteritis. Formula-fed: More rapid diversification but may lack protective “pioneer” phages
Antibiotic use	“Viral collapse”: Loss of bacterial hosts leads to secondary phage depletion; induction of prophages (lytic cycle)	Reduced richness and a “bloom” of antibiotic-resistance genes within the viral reservoir; long-term instability
Social environment	Presence of older siblings and pets acts as a vector for “socially transmitted” eukaryotic viruses	Increased eukaryotic viral richness at 1-2 years; potentially beneficial “immune training” through non-pathogenic exposure
Geography	Urban vs. Rural: Rural living is associated with higher viral diversity and distinct metabolic gene profiles (vAMGs)	Rural viromes tend to converge toward a stable “adult-like” state more resiliently than urban counterparts
Host maturity (age)	Shift from a phage-dominated (predatory) state to a eukaryotic-inclusive (commensal) state	Conversion from chaotic/volatile infancy to a stable, “adult-like” personal virome by age 2 to 5

CMV: Cytomegalovitrus; CS: Cesarean section; HMOs: Human milk oligosaccahrides; TTV: Torque teno virus; vAMGs: Viral auxiliary metabolic genes; VD: Naginal delivery.

Table 3 Viral-host immune interactions in the paediatric gut: Mechanisms, immune pathways, and clinical implications

Virome function	Key viral components	Host sensors/pathways	Primary immune effects	Clinical relevance
Innate immune priming (“tonic signaling”)	Bacteriophages; eukaryotic viruses	TLR9 (DNA); TLR3 (dsRNA); TLR7/8 (ssRNA) on IECs and dendritic cells	Basal interferon signaling; immune readiness without inflammation	Proper immune imprinting during the first 1000 days
Immune sensing and pattern recognition	Phage DNA; viral RNA/DNA	PRRs (TLRs, downstream interferon pathways)	Distinction between commensals and pathogens	Failure may predispose to immune dysregulation
Mucosal barrier reinforcement	Mucus-adherent bacteriophages	Bacteriophage adherence to mucus; epithelial junction signaling	Interception of invading bacteria; enhanced tight junction integrity	Protection against “leaky gut” and microbial translocation
Maintenance of immune tolerance	Commensal viruses (e.g., Anelloviridae)	Induction of regulatory immune pathways	Promotion of Treg differentiation; suppression of unnecessary inflammation	Reduced risk of food allergy and inflammatory disorders
Immune activation (pathological)	Viral overgrowth; phage lytic blooms	Excess PRR stimulation; cytokine release	Pro-inflammatory cytokine production; tissue injury	NEC, IBD, post-infectious inflammation
Immune maturation and adaptive transition	Early-life eukaryotic viruses	Adaptive immune control over viral load	Development of immune competence and stability	Long-term immune programming
Long-term immune programming	Early virome composition	Host-virome co-adaptation	Adult-like immune homeostasis	Dysregulation linked to allergy and autoimmunity
Viral translocation and systemic signaling	Limited passage of viral particles, bacteriophages, or viral nucleic acids across the intestinal barrier into the lamina propria and systemic circulation, particularly during early life or barrier disruption	Pattern recognition receptors (TLR3, TLR7/8, cGAS-STING), type I and III interferon signaling, dendritic cell and monocyte activation	Immune education, and calibration of antiviral immunity and peripheral immune tolerance during critical windows of immune development	Immune maturation and calibration of systemic antiviral responses; excessive translocation linked to systemic inflammation, necrotizing enterocolitis, inflammatory bowel disease, and extra-intestinal immune dysregulation

This table summarizes the principal mechanisms through which the paediatric gut virome interacts with the host immune system. Viral components, including bacteriophages and eukaryotic viruses, engage innate immune sensors to provide tonic immune priming essential for early-life immune imprinting. The virome also contributes to mucosal barrier integrity, promotes immune tolerance through regulatory pathways, and supports adaptive immune maturation. Disruption of these balanced interactions may result in pathological immune activation and contribute to inflammatory gastrointestinal and systemic diseases in childhood. In addition to local gut effects, the paediatric virome can influence systemic immunity through controlled viral translocation and immune signaling. This mechanism highlights the role of the gut virome as a long-range modulator of immune development beyond the gastrointestinal tract. cGAS-STING: Cyclic GMP-AMP synthase-stimulator of interferon genes; TLR: Toll-like receptor; IFN: Interferon; PRR: Pattern recognition receptor; IEC: Intestinal epithelial cell; Treg: Regulatory T cell; IBD: Inflammatory bowel disease; NEC: Necrotizing enterocolitis; HGT: Horizontal gene transfer; ssDNA: Single-stranded DNA; dsRNA: Double-stranded RNA.

Table 4 Modifiers of the paediatric virome

Modifier	Key impact on virome	Long-term consequence
Antibiotics	SOS response and prophage induction	Bacterial instability; expansion of ARGs
Breast milk	Transfer of sIgA and maternal phages	Enhanced barrier protection; regulated assembly
Oral vaccines	Competition with resident viruses	Potential for altered vaccine “take” and immune priming
NICU Stay	Reduced diversity; hospital signatures	Increased risk of NEC and delayed immune maturation

NICU: Neonatal intensive care unit; ARGs: Antibiotic-resistance genes; NEC: Necrotizing enterocolitis; SIgA: Secretory IgA.

Table 5 Localized gastrointestinal disorders and the pediatric virome

Condition	Primary virome alterations (effects)	Putative biological mechanism
Acute gastroenteritis	High load of Reoviridae (Rotavirus), Caliciviridae (Norovirus)	Mucosal Imprinting: Incomplete clearance leads to prolonged immune activation and “sculpting” of future immune tone
Inflammatory bowel disease	Expansion of Caudoviricetes; Contraction of overall viral diversity	Lytic pressure and HGT: Phage blooms deplete beneficial bacteria (e.g., Faecalibacterium prausnitzii) and transfer virulence genes via horizontal gene transfer
Necrotizing enterocolitis	Sudden “phage blooms” preceding symptoms; Low virome stability	The triple hit: Antibiotic-induced SOS response triggers phage lysis; viral translocation across leaky barrier activates TLR-mediated necrosis
Celiac disease	Presence of candidate viruses (Reovirus, Enterovirus)	Loss of Tolerance: Viruses act as “danger signals” that disrupt oral tolerance to gluten, triggering Th1-mediated immune priming in HLA-susceptible children
Functional gastrointestinal disorders	Specific early-life signatures; post-infectious viral “shadows”	Neuro-immune sensitization: Low-grade inflammation and viral-neural crosstalk sensitize nociceptors, leading to visceral hypersensitivity

HGT: Horizontal gene transfer; Th1: T-helper 1 lymphocyte; HLA: Human leukocyte antigen; TLR: Toll-like receptor.

Table 6 Systemic and extra-intestinal effects

Condition	Primary virome alterations (effects)	Putative biological mechanism
Obesity and insulin resistance	Reduced viral diversity; altered phage-to-bacteria ratios	Metabolic supervision: Phages modulate the abundance of SCFA-producing bacteria, influencing energy harvest and systemic lipid metabolism
Type 1 diabetes	Enteroviral persistence; altered phage communities	Molecular mimicry and priming: Enteroviruses may directly target beta cells, while phages prime the innate immune system toward pancreatic autoimmunity
Neurodevelopment (ASD/ADHD)	Distinct viral “fingerprints”; reduced phage diversity	Microglial activation: Gut-derived viral signals influence neuroinflammation and aberrant synaptic pruning during critical developmental windows
Allergy and asthma	Low infantile viral diversity; absence of “Old Friend” commensal viruses	Th2 skewing: Lack of viral-driven Th1/Treg induction prevents the correction of neonatal Th2 bias; disrupted Gut-Lung Axis signaling

ASD/ADHD: Autism spectrum disorders/attention deficit hyperactivity disorders; SCFA: Short-chain fatty acids; Th1: T-helper 1 lymphocyte; Th2: T-helper 1 lymphocyte.

Table 7 Summary of clinical frontiers

Modality	Strategy	Primary advantage
Biomarkers	Viral “Fingerprinting”	Early detection before symptoms or bacterial shifts. AI-driven “Early Warning Systems” for high-risk neonates
Phage therapy	Targeting pathobionts	Highly specific; preserves the “good” microbiome. Routine “precision editing” for pathobiont-driven IBD
FVT	Sterile filtrate transfer	Safer than whole-fecal transplants for children. FVT is a primary “reset” for metabolic and immune health
Nutrition	Indirect modulation	Scalable and low risk for long-term health

FVT: Fecal viral transplantation; IBD: Inflammatory bowel disease.

Table 8 Technical bottlenecks in paediatric viromics

Step	Challenge	Impact on pediatric research
Sample collection	Low volume (especially from neonates)	Limits the ability to perform multiple enrichment steps
Viral enrichment	Distinguishing “free” viruses from prophages	Makes it hard to tell if a virus is active or just dormant in a bacterium
Sequencing	High cost of deep metagenomics	Reduces the sample size of studies, often leading to “underpowered” results
Bioinformatics	Lack of universal markers	Prevents the easy, high-throughput identification possible with 16S sequencing

Table 9 The roadmap for future research

Research frontier	Current status	Future goal
Dark matter	90% uncharacterized	Comprehensive viral reference catalogs
Study design	Cross-sectional “snapshots”	Multi-decade longitudinal tracking.
Mechanisms	Purely associative	Proof-of-concept in organoids and GF models
Therapeutics	Experimental/compassionate	Phase III clinical trials in paediatric IBD/NEC

GF: Germ-free; IBD: Inflammatory bowel disease; NEC: Necrotizing enterocolitis.