Gut microbiome in Bangladeshi mother-infant pairs, cohort

Human-associated microbes are a key determinant of human health, development and disease. For instance, microbial communities in the human gut play a vital role in host metabolism and in the stimulation and development of the host innate immune system. Perturbations to these microbial assemblies, referred to as dysbiosis, are linked to negative health outcomes including allergies, obesity, undernutrition and early childhood sepsis. Most of what we know about the microbiome comes from high-income settings. This is because, low- and middle-income countries (LMICs) are currently underrepresented in global microbiome study. In addition, recent work highlights the influence of geography on the composition and stability of the gut microbiota. For example, Prevotella, prevalent in LMICs, is virtually absent in high-income countries. Even within LMICs, the relative abundance of Prevotella varies substantially. For instance, among Bangladeshi children the presence of Prevotella is far below that in children from Mali, Kenya and The Gambia. This study will describe the composition, diversity, stability, and metabolic activity of gut and body microorganisms in Bangladeshi mother-infant pairs and examine how each of these characteristics vary temporally and by body habitat, mode of delivery, exposure to antibiotics and maternal, infant and household characteristics. In addition, it will examine the human milk oligosaccharide (HMO) profile of breast milk collected from lactating women in Bangladesh and examine how HMO profile varies temporally, and by secretor status, maternal age, parity, diet, mode of delivery, season of milk collection, infant feeding pattern, and other maternal, infant and household characteristics. This will help us understand the relationship between mother and infant gut and body microbial communities over time and in the early postnatal period, gut microbiomes and microbial derived metabolites in mother-infant pairs and finally, HMO profiles and the composition of the infant gut microbiome.

Classified as human gut / stool / human milk / oral cavity / skin shotgun DNA metagenome of infant / toddler and child and adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.

• host external_curation.infant_catalog · “infant triage verdict include”
• body site study.description · “in the human gut play a vital”
• body site external_curation.infant_catalog · “infant triage verdict include (gut/stool scope)”
• body site study.description · “will examine the human milk oligosaccharide (HMO) profile”
• body site run.scientific_name · “human oral metagenome”
• body site run.scientific_name · “human skin metagenome”
• life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
• life stage study.description · “in Bangladeshi mother- infant pairs and examine”
• life stage study.description · “undernutrition and early childhood sepsis. Most of”
• life stage study.description · “to antibiotics and maternal , infant and”

1,917 runs over 1,609 samples · mean 0.45 Gbp per run (median 0.40 Gbp, total 857.75 Gbp; 1,917 runs with a base count) · layout PAIRED 1,917 · platform ILLUMINA 1,917 · models Illumina NovaSeq 6000 (1,917) · 7% of runs with a Sandpiper profile · first public 2025-08-12

Freitas AC first · Li G · Shawon J · Qamar H · Pell LG · Kabir M · Oduaran OH · Puebla-Barragan S · Bassani DG · O'Callaghan KM · Onuora JC · Loutet MG · Heasley C · Starke CWE · Mahmud AA · Hamer DH · Pullenayegum E · Hossain MI · Siddiqui MM · Islam MS · Sherman PM · Shah PS · Gaffar SMA · Sultana S · Morris SK · Ahmed T · Haque R · Sarker SA · Roth DE last

PRJEB83236.csv.gz (47.6 KB) · parquet (135.5 KB) — all 1,609 samples, every field with route and confidence · PRJEB83236_determinations.csv.gz (162.9 KB) — 19,292 evidence rows