Data for: Gut Microbiome in Infancy Predicts Malaria Susceptibility

This dataset contains the processed microbiome data and metadata supporting the analyses reported in Dutton et al., "Gut Microbiome in Infancy Predicts Malaria Susceptibility," currently under review at Frontiers in Cellular and Infection Microbiology. Study: A prospective longitudinal cohort of 47 mother-infant dyads recruited at birth in malaria-endemic eastern Democratic Republic of Congo. Infant fecal samples were collected at six weeks, three months, six months, and twelve months of age, as well as at passive malaria sick and post-treatment visits. Full-length 16S rRNA sequencing was performed on PacBio circular consensus sequencing reads across two SMRT cells, and the reads were processed through the DADA2 framework (primer trimming with F27/R1492, length filtering 1000-1600 bp with maxEE=2, PacBio error model, bimera removal, taxonomic assignment against SILVA v138.1). Files: psCombinedCongo_V5.rds - A phyloseq S4 R object containing the OTU table (8,975 taxa x 245 samples), taxonomy table (kingdom through species), and sample metadata including infant ID, timepoint, malaria status variables (BeforeMalaria, DuringMalaria, PostMalaria), bednet use, antibiotic exposure, infant sex, and related covariates. This object is the merged product of two sequencing rounds. working_malaria_risk_score.csv - Per-infant composite malaria risk scores (range 0-6) derived from household questionnaire data covering bednet use, antimalarial drug use during pregnancy, maternal and household malaria cases, and environmental risk. Used as a covariate in the k-NN classifier sensitivity analyses. Reproducibility: These data files are the inputs to the R Markdown analysis pipeline archived separately at Zenodo (see Related identifiers). The full upstream DADA2 sequence processing pipeline that generated psCombinedCongo_V5.rds from raw PacBio FASTQ files is also included in the archived code repository. The analysis pipeline uses renv to pin exact package versions; running renv::restore() followed by knitting the analysis Rmd reproduces all main figures (1-7), supplemental figures (S1-S4), classifier analyses, validation analyses, and statistical results reported in the manuscript.Raw sequence data: Raw PacBio CCS reads are deposited with the NCBI Sequence Read Archive (to be released upon publication of the associated manuscript)