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PRJNA217052 SRP029441

Human-animal microbiome sharing, cross-sectional, Fiji

Fiji COMP

Cross-sectional study of 522 samples from people and their domestic animals in Fiji, examining sharing of gut, mouth, and skin bacteria; 171 samples are from healthy controls. machine-written summary

484 samples · 8,503 runs · FJ · Age unknown · 2015 · 0.99 Gbp / sample

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Sources
✓Sequence archive 276✓Abstract / description 75○Full text✓Supplementary tables 848✓External resources 785–User contribution–Human verified

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

what each source gave
✓ Sequence archive276 sample values (subject id)
✓ Abstract / description75 sample values (country)
○ Full textread; no usable statement or table · PMC10154212, PMC10258454, PMC10865984, PMC11514259, PMC11980382, PMC12297358, PMC13269251, PMC4720164, PMC4983458, PMC5007149, PMC6424576, PMC7000725, PMC7450247, PMC7702799, PMC8062976, PMC9684161, PMC9975273
✓ Supplementary tables848 sample values (country, health condition, health condition detail, sex, timepoint)
✓ External resources785 sample values (age, country, health condition, health condition detail, sex) · 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 country
Age
unknown323
adult132
adolescent13
elderly11
child5
Condition
healthy_control307
Sex
female110
male57
Country
FJ484
Body site
excluded243
primary241
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 %)this project, 0.1–0.3 Gbp: 1 samplesall projects, 0.3–1 Gbp: 47,044 samples (8 %)this project, 0.3–1 Gbp: 115 samplesall projects, 1–3 Gbp: 124,983 samples (22 %)this project, 1–3 Gbp: 119 samplesall projects, 3–10 Gbp: 253,728 samples (44 %)this project, 3–10 Gbp: 119 samplesall projects, 10–30 Gbp: 72,533 samples (13 %)this project, 10–30 Gbp: 130 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 4.04 Gbp per sample0130Gbp
! Self-contradictory metadata

sex differs between samples of the same subject id (70 subjects, 140 samples) — sex withheld; subject ids shared by samples of both sexes (70 ids, 140 samples) — ids withheld.

The sources disagree on 140 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 280)
samplefieldvalueother valuehandling
SAMN02333917sexmale (curatedMetagenomicData)subject W1.9: male in 1 sample, female in 1 samplewithheld: neither value published
SAMN02333920sexfemale (curatedMetagenomicData)subject M1.61: female in 1 sample, male in 1 samplewithheld: neither value published
SAMN02333921sexfemale (curatedMetagenomicData)subject M1.64: female in 1 sample, male in 1 samplewithheld: neither value published
SAMN02333922sexfemale (curatedMetagenomicData)subject M2.38: female in 1 sample, male in 1 samplewithheld: neither value published
SAMN02333924sexfemale (curatedMetagenomicData)subject M2.45: female in 1 sample, male in 1 samplewithheld: neither value published
SAMN02333936sexmale (curatedMetagenomicData)subject W2.4: male in 1 sample, female in 1 samplewithheld: neither value published
SAMN02333941sexfemale (curatedMetagenomicData)subject M2.57: female in 1 sample, male in 1 samplewithheld: neither value published
SAMN02333942sexmale (curatedMetagenomicData)subject W1.39: male in 1 sample, female in 1 samplewithheld: neither value published
SAMN02333946sexmale (curatedMetagenomicData)subject W2.61: male in 1 sample, female in 1 samplewithheld: neither value published
SAMN02333948sexmale (curatedMetagenomicData)subject W3.20: male in 1 sample, female in 1 samplewithheld: neither value published
SAMN02333956sexfemale (curatedMetagenomicData)subject M1.6: female in 1 sample, male in 1 samplewithheld: neither value published
SAMN02333960sexfemale (curatedMetagenomicData)subject M2.40: female in 1 sample, male in 1 samplewithheld: neither value published
SAMN02333961sexfemale (curatedMetagenomicData)subject M2.41: female in 1 sample, male in 1 samplewithheld: neither value published
SAMN02333962sexfemale (curatedMetagenomicData)subject M2.56: female in 1 sample, male in 1 samplewithheld: neither value published
SAMN02333965sexmale (curatedMetagenomicData)subject W2.19: male in 1 sample, female in 1 samplewithheld: neither value published
SAMN02333966sexmale (curatedMetagenomicData)subject W2.23: male in 1 sample, female in 1 samplewithheld: neither value published
SAMN02333968sexmale (curatedMetagenomicData)subject W2.40: male in 1 sample, female in 1 samplewithheld: neither value published
SAMN02333969sexmale (curatedMetagenomicData)subject W3.19: male in 1 sample, female in 1 samplewithheld: neither value published
SAMN02333970sexmale (curatedMetagenomicData)subject W3.22: male in 1 sample, female in 1 samplewithheld: neither value published
SAMN02333986sexmale (curatedMetagenomicData)subject W2.59: male in 1 sample, female in 1 samplewithheld: neither value published
SAMN02333996sexfemale (curatedMetagenomicData)subject M1.10: female in 1 sample, male in 1 samplewithheld: neither value published
SAMN02333997sexfemale (curatedMetagenomicData)subject M1.44: female in 1 sample, male in 1 samplewithheld: neither value published
SAMN02334001sexmale (curatedMetagenomicData)subject W2.36: male in 1 sample, female in 1 samplewithheld: neither value published
SAMN02334004sexmale (curatedMetagenomicData)subject W2.54: male in 1 sample, female in 1 samplewithheld: neither value published
SAMN02334005sexmale (curatedMetagenomicData)subject W2.63: male in 1 sample, female in 1 samplewithheld: neither value published
SAMN02334016sexfemale (curatedMetagenomicData)subject M1.4: female in 1 sample, male in 1 samplewithheld: neither value published
SAMN02334017sexmale (curatedMetagenomicData)subject W1.1: male in 1 sample, female in 1 samplewithheld: neither value published
SAMN02334019sexmale (curatedMetagenomicData)subject WL.2: male in 1 sample, female in 1 samplewithheld: neither value published
SAMN02334021sexfemale (curatedMetagenomicData)subject M1.16: female in 1 sample, male in 1 samplewithheld: neither value published
SAMN02334025sexfemale (curatedMetagenomicData)subject M1.57: female in 1 sample, male in 1 samplewithheld: neither value published
SAMN02334027sexfemale (curatedMetagenomicData)subject M2.37: female in 1 sample, male in 1 samplewithheld: neither value published
SAMN02334030sexmale (curatedMetagenomicData)subject W1.36: male in 1 sample, female in 1 samplewithheld: neither value published
SAMN02334036sexfemale (curatedMetagenomicData)subject M1.1: female in 1 sample, male in 1 samplewithheld: neither value published
SAMN02334037sexmale (curatedMetagenomicData)subject W1.4: male in 1 sample, female in 1 samplewithheld: neither value published
SAMN02334038sexfemale (curatedMetagenomicData)subject M1.26: female in 1 sample, male in 1 samplewithheld: neither value published
SAMN02334040sexfemale (curatedMetagenomicData)subject M2.49: female in 1 sample, male in 1 samplewithheld: neither value published
SAMN02334043sexmale (curatedMetagenomicData)subject W2.67: male in 1 sample, female in 1 samplewithheld: neither value published
SAMN02334049sexfemale (curatedMetagenomicData)subject M1.8: female in 1 sample, male in 1 samplewithheld: neither value published
SAMN02334051sexfemale (curatedMetagenomicData)subject M1.38: female in 1 sample, male in 1 samplewithheld: neither value published
SAMN02334052sexfemale (curatedMetagenomicData)subject M1.42: female in 1 sample, male in 1 samplewithheld: neither value published
Sampling design and relatedness

community — not resolvedhouseholds — not resolvedparent–child — not resolvedpartners / couples — not resolved

287 villagers in 5 Fijian villages with household, spouse and mother-child links (paper); links not retrieved.

How longitudinal and relatedness information is derived

Community composition
Prevotella 22.9%Faecalibacterium 4.3%Roseburia 4.0%Phocaeicola 3.9%Succinivibrio 3.2%Bacteroides 2.6%Alloprevotella 1.6%Cryptobacteroides 1.4%Lachnospira 1.2%Acetatifactor 1.1%Bifidobacterium 1.1%Dialister 0.9%not assigned to a genus 26.6%other genera 25.3%

Genera, mean relative abundance over 278 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage
fieldsamplescoverageR1R2R3R4
age_category161 33%
country484 100%40975
health_condition307 63%307
subject_id276 57%276
health_condition_detail307 63%307
timepoint_label272 56%272
age_at_collection_days171 35%171
sex167 35%167
Papers (17)
  • Detection of low-abundance bacterial strains in metagenomic datasets by eigengenome partitioning. 2015 PMID 26368049 PMC4720164 own_data
  • Mobile genes in the human microbiome are structured from global to individual scales. 2016 PMID 27409808 PMC4983458 own_data
  • Virtual microfluidics for digital quantification and single-cell sequencing. 2016 PMID 27479330 PMC5007149 own_data
  • Transmission of human-associated microbiota along family and social networks. 2019 PMID 30911128 PMC7450247 own_data
  • G2S: A New Deep Learning Tool for Predicting Stool Microbiome Structure From Oral Microbiome Data. 2021 PMID 33897763 PMC8062976 own_data
12 more
  • <i>Prevotella copri</i> variants among a single host diverge in sphingolipid production. 2024 PMID 38236049 PMC10865984
  • Segatella clades adopt distinct roles within a single individual's gut. 2024 PMID 39465298 PMC11514259
  • Extensive transmission of microbes along the gastrointestinal tract. 2019 PMID 30747106 PMC6424576
  • Abundance and diversity of resistomes differ between healthy human oral cavities and gut. 2020 PMID 32019923 PMC7000725
  • Metagenomics of the modern and historical human oral microbiome with phylogenetic studies on <i>Streptococcus mutans</i> and <i>Streptococcus sobrinus</i>. 2020 PMID 33012228 PMC7702799
  • Over 50,000 Metagenomically Assembled Draft Genomes for the Human Oral Microbiome Reveal New Taxa. 2022 PMID 34492339 PMC9684161
  • The human microbiome encodes resistance to the antidiabetic drug acarbose. 2021 PMID 34819672 PMC10258454
  • Enrichment of oral-derived bacteria in inflamed colorectal tumors and distinct associations of Fusobacterium in the mesenchymal subtype. 2023 PMID 36706753 PMC9975273
  • Toward an improved definition of a healthy microbiome for healthy aging. 2022 PMID 37118093 PMC10154212
  • The physical biogeography of <i>Fusobacterium nucleatum</i> in health and disease. 2025 PMID 40062772 PMC11980382
  • Integrating metagenomics and cultivation unveils oral phage diversity and potential impact on hosts. 2025 PMID 40715125 PMC12297358
  • Strain transmission links human microbiomes along the oral-gut axis and across cohabiting individuals. 2026 PMID 42312244 PMC13269251
Details
Archive description

This study will characterize the role of human-associated bacteria in health and disease from a sample set collected in Fiji. The study seeks to find out how people share benign bacteria that live in guts, mouths and skin with each other and with their domestic animals and surroundings. There are several diseases that are spread by bacteria between humans and between humans and their livestock. Through this study, the researchers want to determine how much bacterial sharing goes on between humans and their domestic animals.

How this project entered the registry

Classified as human and non-human (mixed) gut / stool / oral cavity / skin / other human site shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.60. Assay shotgun_dna.

  • host study.description · “between humans and their domestic animals”
  • host run.scientific_name · “soil metagenome”
  • body site study.description · “live in guts, mouths and skin”
  • body site run.scientific_name · “oral metagenome”
Evidence examples (one per field × route)
samplefieldvaluerouteconf.sourcequote
SAMN02333917age_at_collection_days9131.25R20.75external.cmd sourceage: 25; age_unit: Year; age_group: Adult
SAMN02333917countryFJR20.75external.cmd sourcecountry: Fiji
SAMN02334085countryFJR20.75paper.supp.41467_2020_14422_MOESM5_ESM.csv[!Country]Country: Fiji
SAMN02333929countryFJR40.50study.descriptionsample set collected in Fiji
SAMN02333917health_conditionhealthy_controlR20.75external.cmd sourcedisease: Healthy
SAMN02334085health_conditionhealthy_controlR20.75paper.supp.41467_2020_14422_MOESM5_ESM.csv[!Health]Health: healthy
SAMN02333917health_condition_detailHealthyR20.75external.cmd sourcedisease: Healthy
SAMN02334085health_condition_detailhealthyR20.75paper.supp.41467_2020_14422_MOESM5_ESM.csv[!Health]Health: healthy
SAMN02333918sexfemaleR20.75external.cmd sourcesex: Female
SAMN02334129sexfemaleR20.75paper.supp.41467_2020_14422_MOESM5_ESM.csv[!Sex]Sex: F
SAMN02333918subject_idW2.7R10.70sample.name_rule:aliasW2.7.ST
SAMN02333917timepoint_label1R20.75paper.supp.41467_2020_14422_MOESM5_ESM.csv[!Visit_Number]Visit_Number: 1
Sequencing

8,503 runs over 484 samples · mean 0.34 Gbp per run (median 0.11 Gbp, total 2,894.96 Gbp; 8,503 runs with a base count) · layout PAIRED 8,503 · platform ILLUMINA 8,503 · models Illumina HiSeq 2000 (8,503) · 46% of runs with a Sandpiper profile · first public 2015-08-29 – 2015-12-10

Authors (57)

Orihara K first · Yahagi K · Saito Y · Watanabe Y · Sasai T · Hara T · Tsukuda N · Oki K · Fujimoto J · Matsuki T last · Xiao X first · Le HH · Lee MT · Lamm D · Johnson EL · Brito IL last · Singh A · Giometto A · Connolly JP first · Kelly L last · Jie Z first · Liang H · Meng Y · Zhang J · Zhang T · Li W · Lin X · Hu T · Han M · Liang W · Ju Y · Tong X · Jin X · Xu X · Zhang W · Wang J · Yang H · Kristiansen K · Xiao L · Zou Y last · Heidrich V first · Fackelmann G · Ricci L · Spadazzi R · Baldanzi G · Punčochář M · Catassi G · Marchi P · Modesto M · Piccinno G · Porcari S · Rondinella D · Asnicar F · Valles-Colomer M · Mattarelli P · Ianiro G · Segata N last

Downloads

PRJNA217052.csv.gz (13.4 KB) · parquet (89.3 KB) — all 484 samples, every field with route and confidence · PRJNA217052_determinations.csv.gz (19.8 KB) — 1,984 evidence rows

Samples (484 · every field this project has values for · hover a cell for its source)
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