Long-read metagenomics of infant gut samples, Malawi/USA
Long read metagenomics
544 fecal samples, mostly from infants in Malawi (Masinjere, Limera) with some from San Diego, USA, profiled using long-read (PacBio, ONT) and short-read sequencing in a cross-sectional comparative study. machine-written summary
Sequencing depth per sample · this project all projects
Sampling design and relatedness
longitudinalcommunity
50 of 50 people sampled more than once (533 samples; median 10, up to 22 per person) · follow-up median 11 mo (max 9.5 y) · median interval between samples 3 mo(time from age at collection).
Schedule stated by the source: “Repeated fecal sampling of same 50 infants at multiple ages/timepoints (collection_week: 0,2,6,12,24,36,48)”.
Each row is one person (36 shown of 50); dots are samples at days since that person's first sample.
2 shared settings.
member · circles are people (pale = no sequenced sample), arrows run donor → recipient and parent → child, curved lines join twins, partners and siblings, squares are shared settings or families without recorded roles. Shown: 2 shared settings. 50 people in the project overall.
Prevotella 49.8%Bifidobacterium 5.5%Megasphaera 5.4%Succinivibrio 4.0%Alloprevotella 2.7%Escherichia 2.5%Faecalibacterium 2.2%Dialister 1.8%Ligilactobacillus 1.6%Bacteroides 1.1%Campylobacter_D 1.1%Akkermansia 1.0%not assigned to a genus 3.8%other genera 17.6%
Genera, mean relative abundance over 29 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
Long read (LR) DNA sequencing is revolutionizing comparative genomics of eukaryotes and microbial cultured isolates, but has not been widely adopted in microbial metagenomics due to limitations in throughput, cost, and data quality. Here, we developed a high-throughput, low cost molecular workflow and generated paired, long read DNA sequencing data from 47 complex, human fecal samples with the Pacbio (PB) Revio (591 Gbp), the Oxford Nanopore Technologies (ONT) PromethION (1171 Gbp), and 40 samples with Illumina (ILMN) synthetic long reads (625 Gbp). PB outperformed ONT in most sequencing metrics (% useable data, read quality, mean, median and read length N50), generated 2.43x more complete metagenome-assembled genomes (cMAGs) at the lowest cost per cMAG ($16 USD vs $25), and had the highest profiling classification rates resulting in detecting the most significant associations. Both PB and ONT generated 51 and 72x more cMAGs per Gbp than ILMN. We generated 985 (831 circular) cMAGs, performed whole genome and functional pangenome analyses across ten genera, and identified microbial genetic associations with various environmental and biological phenotypes related to undernutrition in toddlers from sub-Saharan Africa that would not have been possible with short reads.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of infant / toddler by deterministic_prior with confidence 0.90. Assay shotgun_dna.
body sitestudy.description · “47 complex, human fecal samples with the”
body siteexternal_curation.infant_catalog · “infant triage verdict include (gut/stool scope)”
life stageexternal_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
life stagestudy.description · “to undernutrition in toddlers from sub-Saharan Africa”
Evidence examples (one per field × route)
sample
field
value
route
conf.
source
quote
SAMN42799962
age_at_collection_days
707
R1
0.90
biosample_attr
23.23
SAMN42799962
collection_date
2015-07-22
R1
0.85
biosample.attribute:collection_date
2015-07-22
SAMN42799962
country
MW
R1
0.90
biosample_attr
Malawi: Limera
SAMN42799962
sex
male
R1
0.90
biosample_attr
male
SAMN42799962
shared_setting_id
Limera
R1
0.85
biosample.attribute:geo_loc_name
Malawi: Limera
SAMN42799962
shared_setting_type
village_or_community
R1
0.85
biosample.attribute:geo_loc_name
Malawi: Limera
SAMN42799962
subject_id
526
R1
0.85
biosample_attr
526
SAMN42799962
timepoint_label
0
R1
0.80
biosample_attr
0
Sequencing
663 runs over 544 samples · mean 3.98 Gbp per run (median 0.13 Gbp, total 2,641.71 Gbp; 663 runs with a base count) · layout SINGLE 625, PAIRED 38 · platform PACBIO_SMRT 561, OXFORD_NANOPORE 64, ILLUMINA 38 · models Revio (561), PromethION (64), Illumina NovaSeq X (38) · 4% of runs with a Sandpiper profile · first public 2024-08-31 – 2025-06-24