Gut microbiome and growth faltering in Indian infants

A collaborative study between SJRI Bangalore and AIIMS Bhubaneswar.</p><p>Dr Rebecca Raj Kurian</p><p>Professor and Head</p><p>Division of Nutrition</p><p>St. Johns Research Institute</p><p>Dr Balamurugan Ramadass</p><p>Additional Professor</p><p>Dept. of Biochemistry</p><p>AIIMS Bhubaneswar</p><p>Background: Linear growth faltering (LGF) during the first 1000 days predisposes children to lifelong metabolic and developmental consequences. Gut microbial dysbiosis may impair nutrient absorption and growth hormone signaling, yet longitudinal metagenomic evidence linking microbial maturation to body composition in Indian infants remains limited.</p><p>Objectives: We examined longitudinal associations between gut microbiome composition, diversity, functional pathways, and body composition in Indian infants with and without LGF from birth to 12 months.</p><p>Methods: We conducted a prospective cohort study of 32 mother-infant pairs (16 LGF, 16 NLGF) recruited from hospitals and community centers in Bengaluru India. We assessed anthropometry and body composition (body cell mass [BCM] fat mass [FM] fat-free mass [FFM]) at birth 3 6 and 12 months using whole-body potassium counting. Fecal samples underwent wholegenome metagenomic sequencing (Illumina NovaSeq X Plus). We performed taxonomic profiling using Kraken2 and functional annotation using metaSPAdes and Prodigal. We analyzed beta diversity via PERMANOVA differential abundance via MANOVA and microbial body composition associations via linear mixed-effects (LME) models adjusted for sex delivery mode and breastfeeding.</p><p>Results: At 12 months LGF infants exhibited significantly lower weight-for-age z-scores height-for-age z-scores and FFM index. Bifidobacterium bifidum and Blautia wexlerae were enriched in NLGF infants whereas Enterococcus faecium Escherichia coli and Staphylococcus epidermidis were enriched in LGF infants. Microbial network stability was 4-fold lower in LGF infants at 12 months. Functional pathways for amino acid biosynthesis and short-chain fatty acid production were depleted in LGF infants.</p><p>Conclusions: LGF in Indian infants associates with persistent gut microbial dysbiosis characterized by Bifidobacterium depletion pathobiont enrichment and impaired microbial network stability. These microbial alterations correlate with deficits in lean tissue accretion suggesting that early interventions targeting the gut microbiome may improve growth outcomes.

Classified as human gut / stool / skin / blood / tissue / internal fluids shotgun DNA metagenome of infant / toddler and child by deterministic_prior with confidence 0.90. Assay shotgun_dna.

• host external_curation.infant_catalog · “infant triage verdict include”
• body site study.description · “and developmental consequences. Gut microbial dysbiosis may”
• body site external_curation.infant_catalog · “infant triage verdict include (gut/stool scope)”
• body site study.description · “coli and Staphylococcus epidermidis were enriched in”
• body site study.description · “deficits in lean tissue accretion suggesting that”
• life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
• life stage study.title · “faltering in Indian Infants”
• life stage study.description · “1000 days predisposes children to lifelong metabolic”

159 runs over 159 samples · mean 5.65 Gbp per run (median 5.31 Gbp, total 898.38 Gbp; 159 runs with a base count) · layout PAIRED 158, SINGLE 1 · platform ILLUMINA 159 · models Illumina NovaSeq X Plus (159) · 0% of runs with a Sandpiper profile · first public 2026-05-13

No author record.

2 of the 4 core fields are below 50% coverage: age_category, health_condition. Share metadata

PRJNA1452619.csv.gz (5.5 KB) · parquet (77.0 KB) — all 159 samples, every field with route and confidence · PRJNA1452619_determinations.csv.gz (7.6 KB) — 1,113 evidence rows