CHAIN gut metagenomes in hospitalised children, case-control

The Childhood Acute Illness and Nutrition (CHAIN) Network (www.chnnetwork.org) is a global multi-centre study that aims to understand and identify intervenable mechanisms that increase the risk of death among vulnerable children hospitalised in low- and middle-income countries (LMICs). The CHAIN Network recruited and longitudinally sampled a large cohort of children aged 2–24 months (i.e. from breastfed infants to weaned toddlers) with varying degrees of malnutrition presenting to hospital, with mortality rates of ~10% occurring either in hospital or post-discharge. This study spans nine sites in six countries across Africa and South Asia, with unified protocols for sample collection and clinical metadata capture. These samples provide a deeply characterised healthy microbiome baseline in under-sampled populations from Africa and South Asia, enabling comparison with hospital-admitted children to identify biomarkers of malnutrition. This CHAIN nested case-cohort (NCC) metagenomics dataset is the microbiome arm of the NCC study, a subset of CHAIN participants investigating biological mechanisms underlying inpatient and post-discharge mortality through an integrated multi-omic approach (PMID: 36415883). These data are part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/. These data are made available on an open access basis for research use only. Any person wishing to use these data for commercial purposes must first enter into an appropriate commercial licensing and benefit-sharing agreement with the relevant CHAIN participating country. For Malawi, the relevant authority is the Public Health Research Institute, Ministry of Health, Republic of Malawi. The data including metadata associated with the CHAIN NCC study are archived on the Harvard Dataverse (https://doi.org/10.7910/DVN/X6FAGX). The data contain sensitive information about study participants and may include identifiers that could compromise confidentiality or lead to ethnic stigmatisation. Access to these data requires submission of a formal request for consideration by our Data Governance Committee. Email completed data request form to the Data Governance Committee at dgc@kemri-wellcome.org. The requester provides investigators details, variables requested, intended use of the dataset, potential risks of the study including risks to confidentiality of individuals or communities, potential benefits of the study including to participant communities, scientific capacity building or health policy and planned outputs (if analysis on dataset will result in publication or reports or presentations). The requester also needs to formally agree to the conditions and limitations for data sharing to avoid misuse of shared data. Processing of data requests takes between 4 weeks to 6 weeks from submission.

Classified as human gut / stool 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 external_curation.infant_catalog · “infant triage verdict include (gut/stool scope)”
• life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
• life stage study.description · “(i.e. from breastfed infants to weaned toddlers)”
• life stage study.description · “The Childhood Acute Illness and”

1,853 runs over 1,851 samples · mean 4.17 Gbp per run (median 4.35 Gbp, total 7,729.33 Gbp; 1,853 runs with a base count) · layout PAIRED 1,853 · platform ILLUMINA 1,853 · models Illumina NovaSeq 6000 (1,751), Illumina HiSeq 4000 (102) · 98% of runs with a Sandpiper profile · first public 2026-01-28

Espinosa CA first · Njunge JM · Tickell KD · Diallo AH · Sayeem Bin Shahid ASM · Gazi MA · Kazi Z · Yoshioka E · Tigoi C · Mburu M · Ngari M · Ngao N · Omer E · Gumbi W · Gichuki BM · Mitchel A · Williams J · Gogain J · Janjic N · Mandal R · Jenkins B · Browne HP · Shao Y · Rozday T · Stares MD · Dawson NJR · Berson E · Chang A · Kim Y · Mataraso SJ · Shu CH · Phongpreecha T · Xue L · Saleem A · Singa B · Ahmed T · Voskuijl WP · Wishart DS · Houpt ER · Liu J · Ali A · Mupere E · Chisti MJ · Bandsma RHJ · Lawley TD · Koulman A · Lancioni CL · Aghaeepour N · Berkley JA · Walson JL · Childhood Acute Illness and Nutrition (CHAIN) Network last

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

PRJEB106892.csv.gz (53.3 KB) · parquet (156.7 KB) — all 1,851 samples, every field with route and confidence · PRJEB106892_determinations.csv.gz (47.4 KB) — 3,350 evidence rows