Gut microbiome method development, Bangladeshi children and mice
1618 samples, mostly from USA (gnotobiotic mice) with 22 from Bangladesh, studying gut microbiomes linked to child malnutrition; longitudinal design; used to test a sequential co-assembly method for metagenome-assembled genomes. machine-written summary
30 samples · 1,618 runs · BD · Child · 2025 · 2.71 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 134 sample values (collection date, country, latitude, location region, longitude) |
| ✓ Abstract / description | 68 sample values (country, health condition, health condition detail) |
| ○ Full text | read; no usable statement or table · PMC12049710 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal — not resolved
Schedule stated by the source: “Not specified; only described as 'a longitudinal study' without stated timepoints”.
Genera, mean relative abundance over 1,602 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 30 | 100% | ||||
| country | 30 | 100% | 22 | 8 | ||
| health_condition | 30 | 100% | 30 | |||
| subject_id | 0 | 0% | ||||
| collection_date | 30 | 100% | 30 | |||
| health_condition_detail | 30 | 100% | 30 | |||
| latitude | 30 | 100% | 30 | |||
| longitude | 30 | 100% | 30 | |||
| detailed_location | 22 | 73% | ||||
| location_region | 22 | 73% | 22 |
- Sequential co-assembly reduces computational resources and errors in metagenome-assembled genomes. 2025 PMID 40101714 PMC12049710 own_data
Archive description
Generating metagenome-assembled genomes (MAGs) from DNA shotgun sequencing datasets can demand considerable computational resources. Here we describe a sequential co-assembly method that reduces the assembly of duplicate reads through successive application of single-node computing tools for read assembly and mapping. Using a simulated mouse microbiome DNA shotgun sequencing dataset, we demonstrated that this approach shortens assembly time, uses less memory than traditional co-assembly, and produces significantly fewer assembly errors. Applying sequential co-assembly to shotgun sequencing reads from (i) a longitudinal study of gut microbiomes from undernourished Bangladeshi children and (ii) a 2.3 terabyte dataset, generated from gnotobiotic mice colonized with pooled microbiomes from these children, that was too large to be handled by a traditional co-assembly approach, also demonstrated significant reductions in assembly time and memory requirements. These results suggest that this approach should be useful in resource constrained settings, including in low- and middle-income countries.
How this project entered the registry
Classified as human and non-human (mixed) gut / stool shotgun DNA metagenome of child by sonnet_x2 with confidence 0.60. Assay shotgun_dna.
- host study.description · “undernourished Bangladeshi children”
- host run.host_tax_id · “10090”
- body site run.scientific_name · “gut metagenome”
- body site study.description · “gut microbiomes from undernourished Bangladeshi children”
- life stage study.description · “undernourished Bangladeshi children”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN42564774 | collection_date | 2020 | R1 | 0.90 | biosample.attribute:collection_date | 2020 |
| SAMN42564774 | country | BD | R1 | 0.90 | sample.attr.geo_loc_name | Bangladesh |
| SAMN46489374 | country | BD | R4 | 0.50 | paper.abstract | undernourished Bangladeshi children |
| SAMN42564774 | health_condition | malnutrition | R4 | 0.50 | paper.abstract | undernourished Bangladeshi children |
| SAMN42564774 | health_condition_detail | Undernourished children | R4 | 0.50 | paper.abstract | undernourished Bangladeshi children |
| SAMN42564774 | latitude | 23.7100 | R1 | 0.90 | biosample.attribute:lat_lon | 23.71 N 90.41 E |
| SAMN42564774 | location_region | Dhaka | R1 | 0.60 | biosample.attribute:lat_lon | 23.71 N 90.41 E |
| SAMN42564774 | longitude | 90.4100 | R1 | 0.90 | biosample.attribute:lat_lon | 23.71 N 90.41 E |
Sequencing
1,618 runs over 30 samples · mean 2.89 Gbp per run (median 2.71 Gbp, total 4,679.78 Gbp; 1,618 runs with a base count) · layout PAIRED 1,618 · platform ILLUMINA 1,618 · models Illumina NovaSeq 6000 (810), NextSeq 500 (808) · 99% of runs with a Sandpiper profile · first public 2025-03-14 – 2025-03-23
Downloads
PRJNA1137057.csv.gz (1.7 KB) · parquet (70.7 KB) — all 30 samples, every field with route and confidence · PRJNA1137057_determinations.csv.gz (1.7 KB) — 202 evidence rows