Prenatal arsenic exposure, child gut microbiota, Bangladesh
148 samples from Bangladeshi children in a case-control study comparing low versus high prenatal/early-life arsenic exposure from drinking water and its association with intestinal microbiota composition. machine-written summary
149 samples · 149 runs · BD · Child · 2018 · 0.40 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 297 sample values (collection date, country) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 299 sample values (collection date, location locality, location site) · PMC5718612 |
| ○ 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 · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 128 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 | 149 | 100% | ||||
| country | 149 | 100% | 149 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 0 | 0% | ||||
| collection_date | 149 | 100% | 148 | 1 | ||
| detailed_location | 149 | 100% | ||||
| location_locality | 149 | 100% | 149 | |||
| location_site | 149 | 100% | 149 |
- Arsenic exposure and intestinal microbiota in children from Sirajdikhan, Bangladesh. 2017 PMID 29211769 PMC5718612 own_data
Archive description
16s rRNA sequencing Background: Arsenic has antimicrobial properties at high doses yet few studies have examined its effect on gut microbiota. This warrants investigation since arsenic exposure increases the risk for many diseases in which gut microbiota have been shown to play a role. Objective: To examine the role of arsenic exposure early in life on the composition of intestinal microbiota using a nested case-control study of children exposed to low and high arsenic exposure during development (N=50). Methods: Arsenic exposure was measured in maternal drinking water collected <16 weeks gestational age using inductively coupled plasma mass spectrometry. Composition of gut microbiota was evaluated using 16S rRNA gene sequence and shotgun sequencing was performed to evaluate the genomics content of gut microbiota. Results: The gut microbiota in the high arsenic exposure group had increased abundance in Proteobacteria compared to the low exposure group. Furthermore, we identified 332 bacterial genes that were enriched in the high arsenic exposure group and positively correlated with arsenic concentration in drinking water including genes that are involved in virulence and multidrug resistance. Furthermore, over 80% of these genes corresponded to Escherichia coli and Salmonella enterica suggesting that these species were enriched in the high arsenic exposure group. Conclusions: This study provides preliminary data indicating that arsenic exposure early in life was associated with altered gut microbiota in Bangladeshi children. Given the importance of gut microbiota to human health, further studies are needed to confirm this finding and determine the contribution of gut microbiome to arsenic-related diseases.
How this project entered the registry
Classified as human gut / stool / blood / tissue / internal fluids shotgun DNA metagenome of child and adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_child_over_36m”
- body site study.title · “arsenic exposure and intestinal microbiota in Bangladeshi”
- body site study.description · “its effect on gut microbiota. This warrants”
- body site study.description · “using inductively coupled plasma mass spectrometry. Composition”
- life stage external_curation.infant_catalog · “infant triage reason_code age_child_over_36m”
- life stage study.title · “microbiota in Bangladeshi children”
- life stage study.description · “was measured in maternal drinking water collected”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA5065158 | collection_date | 2012-08-07 | R1 | 0.90 | biosample.attribute:collection_date | 2012-08-07 |
| SAMEA5065199 | collection_date | 2013 | R3 | 0.70 | paper.fulltext.methods | In 2013, we conducted a nested study |
| SAMEA5065158 | country | BD | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Bangladesh |
| SAMEA5065158 | location_locality | Sirajdikhan | R3 | 0.70 | paper.fulltext.methods | recruited from within a 15 kilometer radius of Sirajdikhan |
| SAMEA5065158 | location_site | Dhaka Community Hospital affiliated clinics | R3 | 0.70 | paper.fulltext.methods | receiving prenatal care through Dhaka Community Hospital (DCH) affiliated clinics |
Sequencing
149 runs over 149 samples · mean 0.34 Gbp per run (median 0.40 Gbp, total 50.67 Gbp; 149 runs with a base count) · layout SINGLE 149 · platform ILLUMINA 149 · models Illumina HiSeq 2000 (149) · 87% of runs with a Sandpiper profile · first public 2018-11-03
Authors (13)
Dong X first · Shulzhenko N · Lemaitre J · Greer RL · Peremyslova K · Quamruzzaman Q · Rahman M · Hasan OS · Joya SA · Golam M · Christiani DC · Morgun A · Kile ML last
Help complete this project
2 of the 4 core fields are below 50% coverage: health_condition, subject_id. Share metadata
Downloads
PRJEB11852.csv.gz (3.2 KB) · parquet (73.7 KB) — all 149 samples, every field with route and confidence · PRJEB11852_determinations.csv.gz (3.3 KB) — 596 evidence rows