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PRJNA1070670 SRP486509

Pregnant vs non-pregnant gut microbiome, Boston/Cambridge MA

Pregnant vs non-pregnant gut microbiome metagenomic sequencing

Cross-sectional study of 14 stool samples from pregnant and non-pregnant female donors in Boston and Cambridge, Massachusetts, USA, examining gut bacterial conversion of corticoids into progestins. machine-written summary

14 samples · 14 runs · US · Adult · 2024 · 4.20 Gbp / sample

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Sources
✓Sequence archive 154○Abstract / description○Full text○Supplementary tables–External resources–User contribution–Human verified

Checked this project's papers and archive records yourself? Mark it human-verified.

what each source gave
✓ Sequence archive154 sample values (age, collection date, country, health condition, health condition detail, latitude, location locality, location region)
○ Abstract / descriptionread; no usable statement
○ Full textread; no usable statement or table · PMC11179439
○ Supplementary tablesfiles read; no table could be matched to the samples
– External resourcesnot covered by the external resources we ingest
– User contributionnothing uploaded yet
– Human verifiednot yet checked by a person · I checked this project — verify it
Samples at a glance
1 sampling locations · 1 country
Age
adult14
Condition
healthy_control7
pregnancy_postpartum7
Sex
female14
Country
US14
Body site
primary14
Collected 2016–2020
2016: 4 samples2018: 2 samples2020: 8 samples20162020
Sequencing depth per sample · this project all projects
all projects, 0–0.03 Gbp: 25,080 samples (4 %)all projects, 0.03–0.1 Gbp: 17,066 samples (3 %)all projects, 0.1–0.3 Gbp: 29,179 samples (5 %)all projects, 0.3–1 Gbp: 47,044 samples (8 %)all projects, 1–3 Gbp: 124,983 samples (22 %)all projects, 3–10 Gbp: 253,728 samples (44 %)this project, 3–10 Gbp: 13 samplesall projects, 10–30 Gbp: 72,533 samples (13 %)this project, 10–30 Gbp: 1 samplesall projects, 30–100 Gbp: 3,024 samples (1 %)all projects, 100–300 Gbp: 106 samples (0 %)all projects, ≥ 300 Gbp: 9 samples (0 %)project median 4.20 Gbp per sample0130Gbp
Community composition
Blautia_A 9.7%Faecalibacterium 8.6%Ruminococcoides 7.3%Bacteroides 4.9%Bifidobacterium 4.7%Roseburia 4.3%Phocaeicola 4.1%Collinsella 3.4%Gemmiger 2.5%Fusicatenibacter 2.3%Mediterraneibacter 2.2%Streptococcus 1.9%not assigned to a genus 5.8%other genera 38.4%

Genera, mean relative abundance over 14 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage
fieldsamplescoverageR1R2R3R4
age_category14 100%
country14 100%14
health_condition14 100%14
subject_id14 100%14
age_at_collection_days14 100%14
collection_date14 100%14
detailed_location14 100%
health_condition_detail14 100%14
latitude14 100%14
location_locality14 100%14
location_region14 100%14
longitude14 100%14
sex14 100%14
Papers (1)
  • Gut bacteria convert glucocorticoids into progestins in the presence of hydrogen gas. 2024 PMID 38795705 PMC11179439 own_data
Details
Archive description

Metagenomic sequencing of stool samples from pregnant and non-pregnant female donors.

How this project entered the registry

Classified as human gut / stool shotgun DNA metagenome of adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.

  • host external_curation.infant_catalog · “infant triage reason_code age_maternal_only”
  • body site study.title · “Pregnant vs non-pregnant gut microbiome metagenomic sequencing”
  • body site study.description · “Metagenomic sequencing of stool samples from pregnant”
  • life stage external_curation.infant_catalog · “infant triage reason_code age_maternal_only”
Evidence examples (one per field × route)
samplefieldvaluerouteconf.sourcequote
SAMN39657084age_at_collection_days9496.5R10.85biosample.attribute:donor_age26
SAMN39657084collection_date2018R10.90biosample.attribute:collection_date2018
SAMN39657084countryUSR10.90sample.attr.geo_loc_nameUSA: Massachusetts, Cambridge
SAMN39657084health_conditionhealthy_controlR10.70sample.name_rule:aliasnon-preg_fcs_F1
SAMN39657084health_condition_detailnon-pregR10.70sample.name_rule:aliasnon-preg_fcs_F1
SAMN39657084latitude42.3736R10.90biosample.attribute:lat_lon42.3736 N 71.1097 W
SAMN39657084location_localityCambridgeR10.85biosample.attribute:geo_loc_nameUSA: Massachusetts, Cambridge
SAMN39657084location_regionMassachusettsR10.85biosample.attribute:geo_loc_nameUSA: Massachusetts, Cambridge
SAMN39657084longitude-71.1097R10.90biosample.attribute:lat_lon42.3736 N 71.1097 W
SAMN39657084sexfemaleR10.70sample.name_rule:descriptionnon-pregnant female 1
SAMN39657084subject_idF1R10.70sample.name_rule:aliasnon-preg_fcs_F1 | DESCRIPTION=non-pregnant female 1
Sequencing

14 runs over 14 samples · mean 4.63 Gbp per run (median 4.20 Gbp, total 64.81 Gbp; 14 runs with a base count) · layout PAIRED 14 · platform ILLUMINA 14 · models Illumina NovaSeq 6000 (14) · 100% of runs with a Sandpiper profile · first public 2024-06-30

Authors (13)

McCurry MD first · D'Agostino GD · Walsh JT · Bisanz JE · Zalosnik I · Dong X · Morris DJ · Korzenik JR · Edlow AG · Balskus EP · Turnbaugh PJ · Huh JR · Devlin AS last

Downloads

PRJNA1070670.csv.gz (1.4 KB) · parquet (71.2 KB) — all 14 samples, every field with route and confidence · PRJNA1070670_determinations.csv.gz (2.1 KB) — 154 evidence rows

Samples (14 · every field this project has values for · hover a cell for its source)
Loading the sample table…