Gut microbiome in IBD patients in Dhaka, Bangladesh
Cross-sectional study of 4 gut microbiome samples from IBD patients in Dhaka, Bangladesh, aiming to characterize microbial composition and identify bacteria potentially targetable by antibiotic therapy. machine-written summary
4 samples · 4 runs · BD · Age unknown · 2024 · 5.31 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 32 sample values (collection date, country, health condition, health condition detail, latitude, location locality, location region, longitude) |
| – Abstract / description | no abstract or project description |
| ✓ Full text | 8 sample values (age, sex) · PMC11737359 |
| ○ 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 |
Genera, mean relative abundance over 4 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 | 4 | 100% | ||||
| country | 4 | 100% | 4 | |||
| health_condition | 4 | 100% | 4 | |||
| subject_id | 0 | 0% | ||||
| age_at_collection_days | 4 | 100% | 4 | |||
| collection_date | 4 | 100% | 4 | |||
| detailed_location | 4 | 100% | ||||
| health_condition_detail | 4 | 100% | 4 | |||
| latitude | 4 | 100% | 4 | |||
| location_locality | 4 | 100% | 4 | |||
| location_region | 4 | 100% | 4 | |||
| longitude | 4 | 100% | 4 | |||
| sex | 4 | 100% | 4 |
- A whole-genome metagenomic approach to explore the gut microbiome of inflammatory bowel disease patients in Bangladesh PMC11737359 unsure
Archive description
In Bangladesh, the diagnostic procedure for IBD patients is complex and scarce, and doctors often prescribe broad-spectrum antibiotics based on their prior experiences in the absence of evidence-based therapy. The gut microbiome of Bangladeshi people remains grossly understudied, and no published literature is available on the microbiome composition of IBD patients of Bangladeshi origin. In this research, we present a preliminary characterization of the gut microbial composition of IBD patients from Bangladesh and identify potentially targetable bacteria for antibiotic therapy.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.75. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.title · “Gut Microbiome of Inflammatory Bowel Disease”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN36266748 | age_at_collection_days | 11322.8 | R3 | 0.85 | paper.body.TABLE 1[Age] | 31 |
| SAMN36266748 | collection_date | 2022-01 | R1 | 0.90 | biosample.attribute:collection_date | 2022-01 |
| SAMN36266748 | country | BD | R1 | 0.90 | sample.attr.geo_loc_name | Bangladesh: Dhaka |
| SAMN36266748 | health_condition | ibd_unspecified | R1 | 0.70 | sample.name_rule:sample_alias | IBD1 |
| SAMN36266748 | health_condition_detail | IBD | R1 | 0.70 | sample.name_rule:sample_alias | IBD1 |
| SAMN36266748 | latitude | 23.7761 | R1 | 0.90 | biosample.attribute:lat_lon | 23.7761057 N 90.4113768 E |
| SAMN36266748 | location_locality | Dhaka | R1 | 0.85 | biosample.attribute:geo_loc_name | Bangladesh: Dhaka |
| SAMN36266748 | location_region | Dhaka | R1 | 0.85 | biosample.attribute:geo_loc_name | Bangladesh: Dhaka |
| SAMN36266748 | longitude | 90.4114 | R1 | 0.90 | biosample.attribute:lat_lon | 23.7761057 N 90.4113768 E |
| SAMN36266748 | sex | male | R3 | 0.85 | paper.body.TABLE 1[Sex] | Male |
Sequencing
4 runs over 4 samples · mean 5.10 Gbp per run (median 5.31 Gbp, total 20.39 Gbp; 4 runs with a base count) · layout PAIRED 4 · platform ILLUMINA 4 · models Illumina HiSeq 4000 (4) · 100% of runs with a Sandpiper profile · first public 2024-07-02
Authors (11)
Siam M first · Mondol S · Shakil M · Islam M · Islam I · Saha O · Amiruzzaman · Datta R · Ahmed T · Gomes D · Rahaman M last
Downloads
PRJNA990354.csv.gz (1.0 KB) · parquet (70.2 KB) — all 4 samples, every field with route and confidence · PRJNA990354_determinations.csv.gz (1.0 KB) — 40 evidence rows