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PRJNA521455 SRP184706

Gut microbiome of preschool children in rural Zimbabwe

Fecal microbiomes from a Zimbabwean pre-school population

116 fecal samples from preschool-aged children (1-5 years) across five sites in Zimbabwe, shotgun sequenced to study gut protist diversity in relation to age, sex, and Schistosoma haematobium infection; cross-sectional design. machine-written summary

116 samples · 116 runs · ZW · Child · 2020 · 4.53 Gbp / sample

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Sources
✓Sequence archive 1,168✓Abstract / description 3✓Full text 232✓Supplementary tables 18✓External resources 200–User contribution–Human verified

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

what each source gave
✓ Sequence archive1,168 sample values (age, antibiotic exposure, collection date, country, health condition, health condition detail, latitude, location locality)
✓ Abstract / description3 sample values (health condition detail)
✓ Full text232 sample values (lifestyle, lifestyle detail) · PMC13019894, PMC7118151, PMC8617199
✓ Supplementary tables18 sample values (age)
✓ External resources200 sample values (age, bmi, health condition) · from curatedMetagenomicData 3 (cMD 3)
– 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
child88
infant28
Condition
healthy_control75
other_infection18
malnutrition17
Sex
female59
male57
Country
ZW116
Body site
primary116
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 %)this project, 1–3 Gbp: 1 samplesall projects, 3–10 Gbp: 253,728 samples (44 %)this project, 3–10 Gbp: 115 samplesall projects, 10–30 Gbp: 72,533 samples (13 %)all 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 4.53 Gbp per sample0130Gbp
! Self-contradictory metadata

age: sequence archive and curatedMetagenomicData disagree for 36 samples (e.g. 1461.0 vs 1095.75) — withheld; antibiotic exposure: two sequence archives disagree for 28 samples (e.g. no vs yes) — withheld.

The sources disagree on 55 samples. Where two incompatible values exist for one sample (or one person's samples disagree on sex), neither value is published: the field is left empty here, in the sample sheet and in the downloads. Both sides, with their sources, are in gut_metadata_contradictions.parquet of the data package (what counts as a contradiction).

Contradicted values (40 of 64)
samplefieldvalueother valuehandling
SAMN10888510age1461.0 (sequence archive)1095.75 (curatedMetagenomicData)withheld: neither value published
SAMN10888511age85.0 (sequence archive)986 (supplementary table)withheld: neither value published
SAMN10888515age1095.0 (sequence archive)730.5 (curatedMetagenomicData)withheld: neither value published
SAMN10888516age1095.0 (sequence archive)730.5 (curatedMetagenomicData)withheld: neither value published
SAMN10888517age1461.0 (sequence archive)1095.75 (curatedMetagenomicData)withheld: neither value published
SAMN10888520age1461.0 (sequence archive)1095.75 (curatedMetagenomicData)withheld: neither value published
SAMN10888521age1095.0 (sequence archive)730.5 (curatedMetagenomicData)withheld: neither value published
SAMN10888524age629.0 (sequence archive)365.25 (curatedMetagenomicData)withheld: neither value published
SAMN10888525age1095.0 (sequence archive)730.5 (curatedMetagenomicData)withheld: neither value published
SAMN10888527age1461.0 (sequence archive)1095.75 (curatedMetagenomicData)withheld: neither value published
SAMN10888532age730.5 (sequence archive)550 (supplementary table)withheld: neither value published
SAMN10888534age1461.0 (sequence archive)1095.75 (curatedMetagenomicData)withheld: neither value published
SAMN10888535age70.0 (sequence archive)811 (supplementary table)withheld: neither value published
SAMN10888538age1461.0 (sequence archive)1095.75 (curatedMetagenomicData)withheld: neither value published
SAMN10888544age1058.0 (sequence archive)730.5 (curatedMetagenomicData)withheld: neither value published
SAMN10888548age70.0 (sequence archive)845 (supplementary table)withheld: neither value published
SAMN10888549age1095.0 (sequence archive)730.5 (curatedMetagenomicData)withheld: neither value published
SAMN10888564age730.5 (sequence archive)415 (supplementary table)withheld: neither value published
SAMN10888565age85.0 (sequence archive)1388 (supplementary table)withheld: neither value published
SAMN10888566age85.0 (sequence archive)1023 (supplementary table)withheld: neither value published
SAMN10888568age1461.0 (sequence archive)1095.75 (curatedMetagenomicData)withheld: neither value published
SAMN10888570age1239.2 (sequence archive)876 (supplementary table)withheld: neither value published
SAMN10888580age730.5 (sequence archive)1029 (supplementary table)withheld: neither value published
SAMN10888586age70.0 (sequence archive)895 (supplementary table)withheld: neither value published
SAMN10888588age1533.3 (sequence archive)1917 (supplementary table)withheld: neither value published
SAMN10888594age1095.0 (sequence archive)730.5 (curatedMetagenomicData)withheld: neither value published
SAMN10888601age1386.0 (sequence archive)1095.75 (curatedMetagenomicData)withheld: neither value published
SAMN10888605age1028 (supplementary table)730.5 (curatedMetagenomicData)withheld: neither value published
SAMN10888607age1447 (supplementary table)1095.75 (curatedMetagenomicData)withheld: neither value published
SAMN10888611age1095.0 (sequence archive)730.5 (curatedMetagenomicData)withheld: neither value published
SAMN10888612age1095.0 (sequence archive)1410 (supplementary table)withheld: neither value published
SAMN10888613age1095.0 (sequence archive)1445 (supplementary table)withheld: neither value published
SAMN10888615age1461.0 (sequence archive)1095.75 (curatedMetagenomicData)withheld: neither value published
SAMN10888617age548.0 (sequence archive)365.25 (curatedMetagenomicData)withheld: neither value published
SAMN10888619age11.2 (sequence archive)593 (supplementary table)withheld: neither value published
SAMN10888623age1095.0 (sequence archive)790 (supplementary table)withheld: neither value published
SAMN10888514antibiotic exposureno (sequence archive)yes (sequence archive)withheld: neither value published
SAMN10888517antibiotic exposureno (sequence archive)yes (sequence archive)withheld: neither value published
SAMN10888524antibiotic exposureno (sequence archive)yes (sequence archive)withheld: neither value published
SAMN10888525antibiotic exposureno (sequence archive)yes (sequence archive)withheld: neither value published
Sampling design and relatedness

community

116 pre-school children from 5 villages (Mupfure 43, Chihuri 34, Chakandora 24, Nduna 13, Kaziro 2)5 shared settings.

village or community Mupfure · 43 peoplevillage or community Mupfurenan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenan+23
village or community Chihuri · 34 peoplevillage or community Chihurinan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenan+14
village or community Chakandora · 24 peoplevillage or community Chakandoranan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenan+4
village or community Nduna · 13 peoplevillage or community Ndunanan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenannan — member · 1 samplenan
village or community Kaziro · 2 peoplevillage or community Kazironan — member · 1 samplenannan — member · 1 samplenan

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: 5 shared settings.

How longitudinal and relatedness information is derived

Community composition
Prevotella 43.9%Roseburia 4.9%Faecalibacterium 3.8%Bacteroides 3.0%Acetatifactor 2.9%Alloprevotella 2.3%Succinivibrio 2.3%Phocaeicola 1.7%Ruminococcoides 1.7%Dialister 1.5%Vescimonas 1.3%Alistipes 1.2%not assigned to a genus 4.1%other genera 25.6%

Genera, mean relative abundance over 104 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage
fieldsamplescoverageR1R2R3R4
age_category116 100%
country116 100%116
health_condition110 95%1892
subject_id0 0%
collection_date116 100%116
detailed_location116 100%
health_condition_detail116 100%1133
latitude116 100%116
lifestyle116 100%116
lifestyle_detail116 100%116
location_locality116 100%116
longitude116 100%116
sex116 100%116
shared_setting_id116 100%116
shared_setting_type116 100%116
bmi106 91%106
age_at_collection_days80 69%6020
antibiotic_exposure49 42%49
Papers (4)
  • The gut microbiome but not the resistome is associated with urogenital schistosomiasis in preschool-aged children. 2020 PMID 32242065 PMC7118151 own_data
  • Cross-feeding between intestinal pathobionts promotes their overgrowth during undernutrition. 2021 PMID 34824233 PMC8617199 own_data
  • Diversity and composition of gut protist in young rural Zimbabwean children. 2024 PMID 41908157 PMC13019894 own_data
  • Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits. 2023 PMID 38049420 PMC10696028 unsure
Details
Archive description

Fecal samples were obtained from 116 pre-school children in Zimbabwe, and the DNA content assessed using paired-end sequencing.

How this project entered the registry

Classified as human gut / stool shotgun DNA metagenome of child and infant / toddler 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 · “Fecal microbiomes from a”
  • body site study.description · “Fecal samples were obtained”
  • life stage external_curation.infant_catalog · “infant triage reason_code age_child_over_36m”
  • life stage study.description · “from 116 pre-school children in Zimbabwe, and”
  • life stage sample.attr.raw_age · “3.7 (n=20/116)”
Evidence examples (one per field × route)
samplefieldvaluerouteconf.sourcequote
SAMN10888512age_at_collection_days1826.2R10.85sample.attr.raw_age5
SAMN10888509age_at_collection_days1719R20.85paper.supp.42003_2020_859_MOESM3_ESM.xlsx[sample _metadata!Age_years]4.706365503080082
SAMN10888606age_at_collection_days1095.75R20.75external.cmd sourceage: 3; age_unit: Year; age_group: Child
SAMN10888510antibiotic_exposureyesR10.90biosample_attr1
SAMN10888509bmi16.67R20.75external.cmd sourcebmi: 16.66503284
SAMN10888509collection_date2016-02-01R10.90biosample.attribute:collection_date2016-02-01
SAMN10888509countryZWR10.90sample.attr.geo_loc_nameZimbabwe:Chihuri
SAMN10888509health_conditionother_infectionR10.60biosample_attr1
SAMN10888510health_conditionmalnutritionR20.70external.cmd sourcedisease: Growth Retardation
SAMN10888509health_condition_detailschisto: yesR10.85sample.attr.schisto_status1
SAMN10888622health_condition_detailmixed_case_control: schistosome-infected vs uninfected children; also includes undernourished and adequately nourished sR40.50paper.abstractschistosome-infected versus uninfected children
SAMN10888509latitude-16.9146R10.90biosample.attribute:lat_lon16.914583 S 31.445170 E
SAMN10888509lifestylerural_non_industrializedR30.70paper.fulltext.abstractpreschool-aged children (PSAC) in rural Zimbabwe
SAMN10888509lifestyle_detailrural Zimbabwe preschool childrenR30.70paper.fulltext.abstractpreschool-aged children (PSAC) in rural Zimbabwe
SAMN10888509location_localityChihuriR10.85biosample.attribute:geo_loc_nameZimbabwe:Chihuri
SAMN10888509longitude31.4452R10.90biosample.attribute:lat_lon16.914583 S 31.445170 E
SAMN10888509sexfemaleR10.90sample.attr.sexfemale
SAMN10888509shared_setting_idChihuriR10.85biosample.attribute:villageChihuri
SAMN10888509shared_setting_typevillage_or_communityR10.85biosample.attribute:villageChihuri
Sequencing

116 runs over 116 samples · mean 4.61 Gbp per run (median 4.53 Gbp, total 534.48 Gbp; 116 runs with a base count) · layout PAIRED 116 · platform ILLUMINA 116 · models Illumina HiSeq 4000 (116) · 90% of runs with a Sandpiper profile · first public 2020-03-23

Authors (33)

Osakunor DNM first · Munk P · Mduluza T · Petersen TN · Brinch C · Ivens A · Chimponda T · Amanfo SA · Murray J · Woolhouse MEJ · Aarestrup FM · Mutapi F last · Huus KE first · Hoang TT · Creus-Cuadros A · Cirstea M · Vogt SL · Knuff-Janzen K · Sansonetti PJ · Vonaesch P · Finlay BB last · Yersin S first · Garneau JR · Schneeberger PHH · Osman KA · Cercamondi CI · Muhummed AM · Tschopp R · Zinsstag J · Pfavayi LT first · Sibanda EN · Baker S · Woolhouse M

Downloads

PRJNA521455.csv.gz (4.9 KB) · parquet (77.9 KB) — all 116 samples, every field with route and confidence · PRJNA521455_determinations.csv.gz (14.9 KB) — 1,621 evidence rows

Samples (116 · every field this project has values for · hover a cell for its source)
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