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PRJEB30834 ERP113321

Fecal metagenomes across an urbanization gradient in Cameroon

Human fecal metagenomes of individuals sampled along a small-scale urbanization gradient in Cameroon

267 fecal metagenome samples (228 adult, 39 neonate) from healthy individuals in Cameroon, collected cross-sectionally along an urban-to-rural gradient (Yaounde, Mbalmayo, Ngoantet) to study gut microbiota composition. machine-written summary

267 samples · 267 runs · CM · Adult · 2021 · 2.74 Gbp / sample

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Sources
✓Sequence archive 3,229○Abstract / description✓Full text 151✓Supplementary tables 267–External resources–User contribution–Human verified

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

what each source gave
✓ Sequence archive3,229 sample values (age, antibiotic exposure, bmi, collection date, country, health condition, health condition detail, latitude)
○ Abstract / descriptionread; no usable statement
✓ Full text151 sample values (location region) · PMC8013780
✓ Supplementary tables267 sample values (sex)
– 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
3 sampling locations · 1 country
Age
adult228
neonate39
Condition
healthy_control267
Sex
female150
male117
Country
CM267
Body site
primary267
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: 141 samplesall projects, 3–10 Gbp: 253,728 samples (44 %)this project, 3–10 Gbp: 126 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 2.74 Gbp per sample0130Gbp
! Self-contradictory metadata

age: two sequence archives disagree for 39 samples (e.g. 0.0 vs 15340.5) — withheld.

The sources disagree on 39 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 (39)
samplefieldvalueother valuehandling
SAMEA5245245age0.0 (sequence archive)15340.5 (sequence archive)withheld: neither value published
SAMEA5245246age0.0 (sequence archive)15340.5 (sequence archive)withheld: neither value published
SAMEA5245247age0.0 (sequence archive)7305.0 (sequence archive)withheld: neither value published
SAMEA5245248age0.0 (sequence archive)7305.0 (sequence archive)withheld: neither value published
SAMEA5245257age0.0 (sequence archive)9861.8 (sequence archive)withheld: neither value published
SAMEA5245258age0.0 (sequence archive)9861.8 (sequence archive)withheld: neither value published
SAMEA5245267age0.0 (sequence archive)10227.0 (sequence archive)withheld: neither value published
SAMEA5245268age0.0 (sequence archive)10227.0 (sequence archive)withheld: neither value published
SAMEA5245273age0.0 (sequence archive)19723.5 (sequence archive)withheld: neither value published
SAMEA5245274age0.0 (sequence archive)19723.5 (sequence archive)withheld: neither value published
SAMEA5245307age0.0 (sequence archive)15340.5 (sequence archive)withheld: neither value published
SAMEA5245308age0.0 (sequence archive)15340.5 (sequence archive)withheld: neither value published
SAMEA5245309age0.0 (sequence archive)22280.2 (sequence archive)withheld: neither value published
SAMEA5245310age0.0 (sequence archive)22280.2 (sequence archive)withheld: neither value published
SAMEA5245319age0.0 (sequence archive)6574.5 (sequence archive)withheld: neither value published
SAMEA5245320age0.0 (sequence archive)6574.5 (sequence archive)withheld: neither value published
SAMEA5245345age0.0 (sequence archive)10227.0 (sequence archive)withheld: neither value published
SAMEA5245348age0.0 (sequence archive)12783.8 (sequence archive)withheld: neither value published
SAMEA5245349age0.0 (sequence archive)12783.8 (sequence archive)withheld: neither value published
SAMEA5245352age0.0 (sequence archive)12783.8 (sequence archive)withheld: neither value published
SAMEA5245353age0.0 (sequence archive)12783.8 (sequence archive)withheld: neither value published
SAMEA5245358age0.0 (sequence archive)17532.0 (sequence archive)withheld: neither value published
SAMEA5245359age0.0 (sequence archive)17532.0 (sequence archive)withheld: neither value published
SAMEA5245380age0.0 (sequence archive)17532.0 (sequence archive)withheld: neither value published
SAMEA5245381age0.0 (sequence archive)17532.0 (sequence archive)withheld: neither value published
SAMEA5245390age0.0 (sequence archive)16436.2 (sequence archive)withheld: neither value published
SAMEA5245391age0.0 (sequence archive)16436.2 (sequence archive)withheld: neither value published
SAMEA5245396age0.0 (sequence archive)14975.2 (sequence archive)withheld: neither value published
SAMEA5245397age0.0 (sequence archive)14975.2 (sequence archive)withheld: neither value published
SAMEA5245418age0.0 (sequence archive)19723.5 (sequence archive)withheld: neither value published
SAMEA5245419age0.0 (sequence archive)19723.5 (sequence archive)withheld: neither value published
SAMEA5245452age0.0 (sequence archive)14244.8 (sequence archive)withheld: neither value published
SAMEA5245453age0.0 (sequence archive)14244.8 (sequence archive)withheld: neither value published
SAMEA5245462age0.0 (sequence archive)9861.8 (sequence archive)withheld: neither value published
SAMEA5245463age0.0 (sequence archive)9861.8 (sequence archive)withheld: neither value published
SAMEA5245472age0.0 (sequence archive)9131.2 (sequence archive)withheld: neither value published
SAMEA5245473age0.0 (sequence archive)9131.2 (sequence archive)withheld: neither value published
SAMEA5245480age0.0 (sequence archive)9131.2 (sequence archive)withheld: neither value published
SAMEA5245481age0.0 (sequence archive)9131.2 (sequence archive)withheld: neither value published
Sampling design and relatedness

longitudinal — not resolved

133 of 134 people sampled more than once (266 samples; median 2, up to 2 per person).

How longitudinal and relatedness information is derived

Community composition
Prevotella 22.1%Roseburia 4.2%Succinivibrio 3.8%Faecalibacterium 3.0%Cryptobacteroides 2.8%Bacteroides 2.5%Vescimonas 2.0%Acetatifactor 1.9%Alloprevotella 1.8%Alistipes 1.5%Phocaeicola 1.4%Coprococcus 1.3%not assigned to a genus 7.0%other genera 44.7%

Genera, mean relative abundance over 237 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage
fieldsamplescoverageR1R2R3R4
age_category267 100%
country267 100%267
health_condition267 100%267
subject_id267 100%267
collection_date267 100%267
detailed_location267 100%
health_condition_detail267 100%267
latitude267 100%267
location_locality267 100%267
location_region267 100%116151
longitude267 100%267
sex267 100%267
bmi265 99%265
stool_consistency_bristol265 99%265
age_at_collection_days224 84%224
antibiotic_exposure223 84%223
Papers (2)
  • Changes in the Human Gut Microbiota Associated With Colonization by Blastocystis sp. and Entamoeba spp. in Non-Industrialized Populations. 2021 PMID 33816323 PMC8013780 own_data
  • Codiversification of gut microbiota with humans. 2022 PMID 36108023 PMC10777373 unsure
Details
Archive description

Fecal metagenomes were obtained from healthy adults along a small scale (cca 50 km) urbanization gradient in Cameroon: in an urban (Yaounde), semirural(Mbalmayo) and rural area (Ngoantet). Along with the sequencing data, a range of medical, ethnographical, medical, parasitological, sanitary and biometric data were collected in order to elucidate the factors that shape diversity and composition of fecal microbiota in lowly industrialized settings and identify changes that follow urbanization.

How this project entered the registry

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

  • host external_curation.infant_catalog · “infant triage reason_code age_adult_only”
  • body site study.title · “Human fecal metagenomes of individuals”
  • body site study.description · “Fecal metagenomes were obtained”
  • life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
  • life stage study.description · “obtained from healthy adults along a small”
  • life stage sample.attr.host_age · “0 (n=39/267)”
Evidence examples (one per field × route)
samplefieldvaluerouteconf.sourcequote
SAMEA5245239age_at_collection_days17151.0R10.85sample.attr.host_age47
SAMEA5245239antibiotic_exposurenoR10.60biosample_attr4-6m
SAMEA5245239bmi21.1R10.90sample.attr.host_body_mass_index21.1
SAMEA5245239collection_date2017-05-23R10.90biosample.attribute:collection_date2017-05-23
SAMEA5245239countryCMR10.90sample.attr.geographic_location_country_and_or_seaCameroon
SAMEA5245239health_conditionhealthy_controlR10.90biosample_attrhealthy
SAMEA5245239health_condition_detailhealthyR10.90sample.attr.host_disease_statushealthy
SAMEA5245239latitude3.5178R10.90biosample.attribute:geographic_location_latitude+geographic_location_longitude3.5178 11.5099
SAMEA5245239location_localityMbalmayoR10.85biosample.attribute:geographic_location_region_and_localityCameroon: Mbalmayo
SAMEA5245239location_regionCentreR10.60biosample.attribute:geographic_location_latitude+geographic_location_longitude3.5178 11.5099
SAMEA5245291location_regionCentre RegionR30.70paper.fulltext.methodsregional health districts (Centre region, Approval n°0061)
SAMEA5245239longitude11.5099R10.90biosample.attribute:geographic_location_latitude+geographic_location_longitude3.5178 11.5099
SAMEA5245239sexfemaleR20.75paper.supp.Table_1.xlsx[Suppl_Table_1_final!Sex]F_Beb10: F
SAMEA5245239stool_consistency_bristol3R10.90biosample.attribute:stool_consistency_bristol_scale3
SAMEA5245239subject_idBEB10R10.85sample.attr.host_subject_idBEB10
Sequencing

267 runs over 267 samples · mean 2.99 Gbp per run (median 2.74 Gbp, total 797.03 Gbp; 267 runs with a base count) · layout PAIRED 267 · platform ILLUMINA 267 · models Illumina HiSeq 2500 (267) · 89% of runs with a Sandpiper profile · first public 2021-02-17

Authors (49)

Even G first · Lokmer A · Rodrigues J · Audebert C · Viscogliosi E · Ségurel L · Chabé M last · Suzuki TA first · Fitzstevens JL · Schmidt VT · Enav H · Huus KE · Mbong Ngwese M · Grießhammer A · Pfleiderer A · Adegbite BR · Zinsou JF · Esen M · Velavan TP · Adegnika AA · Song LH · Spector TD · Muehlbauer AL · Marchi N · Kang H · Maier L · Blekhman R · Ko G · Youngblut ND · Kremsner P · Ley RE last · Tarracchini C first · Fontana F · Mancabelli L · Lugli GA · Alessandri G · Turroni F · Ventura M · Milani C last · De Biase R · Bocchio F · Viappiani A · De Conto F · Nouvenne A · Ticinesi A · Bussolati O · Meschi T · Cecchi R · van Sinderen D

Downloads

PRJEB30834.csv.gz (8.7 KB) · parquet (83.1 KB) — all 267 samples, every field with route and confidence · PRJEB30834_determinations.csv.gz (23.8 KB) — 3,647 evidence rows

Samples (267 · every field this project has values for · hover a cell for its source)
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