Gut metagenomes from rural north-eastern Madagascar
Cross-sectional study of 112 stool samples from healthy individuals in two rural villages of north-eastern Madagascar, collected by the MAHERY initiative (2013–2014) and sequenced by Illumina HiSeq 2500. machine-written summary
112 samples · 112 runs · MG · Infant / toddler · 2018 · 4.56 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 388 sample values (age, bmi, country, subject id, timepoint) |
| ✓ Abstract / description | 224 sample values (lifestyle, lifestyle detail) |
| ✓ Full text | 112 sample values (collection date) · PMC6349461 |
| ✓ Supplementary tables | 44 sample values (subject id) |
| ✓ External resources | 448 sample values (antibiotic exposure, health condition, health condition detail, sex) · from curatedMetagenomicData 3 (cMD 3) |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
community — not resolved
112 people from two rural villages in NE Madagascar; per-sample village not stated (library prefixes A/V unexplained).
Genera, mean relative abundance over 96 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 | 112 | 100% | ||||
| country | 112 | 100% | 112 | |||
| health_condition | 112 | 100% | 112 | |||
| subject_id | 77 | 69% | 33 | 44 | ||
| age_at_collection_days | 112 | 100% | 112 | |||
| antibiotic_exposure | 112 | 100% | 112 | |||
| bmi | 112 | 100% | 112 | |||
| collection_date | 112 | 100% | 112 | |||
| health_condition_detail | 112 | 100% | 112 | |||
| lifestyle | 112 | 100% | 112 | |||
| lifestyle_detail | 112 | 100% | 112 | |||
| sex | 112 | 100% | 112 | |||
| timepoint_label | 19 | 17% | 19 |
- Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle. PMID 30661755 PMC6349461 curated
- Temporal changes in gastrointestinal fungi and the risk of autoimmunity during early childhood: the TEDDY study. PMID 35672407 PMC9174155 curated
- Characterization of Bifidobacterium kashiwanohense that utilizes both milk- and plant-derived oligosaccharides. PMID 37188713 PMC10187079 curated
- BilR is a gut microbial enzyme that reduces bilirubin to urobilinogen. PMID 38172624 PMC10769871 curated
- Genomic and ecological approaches to identify the Bifidobacterium breve prototype of the healthy human gut microbiota. PMID 38426063 PMC10902438 curated
Archive description
Stool samples from 112 individuals (two villages) in two rural communities of north-eastern Madagascar. Samples were collected by the Madagascar Health and Environmental Research (MAHERY) initiative between 2013 and 2014, and sequenced with Illumina HiSeq 2500.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of infant / toddler by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage verdict include”
- body site study.title · “Metagenomic sequencing of stool samples from rural”
- body site study.description · “Stool samples from 112”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN09781680 | age_at_collection_days | 11323.0 | R1 | 0.85 | biosample.attribute:host_age | 31 |
| SAMN09781680 | antibiotic_exposure | no | R2 | 0.75 | external.cmd source | antibiotics_current_use: No |
| SAMN09781680 | bmi | 19.59 | R1 | 0.90 | biosample.attribute:host_body_mass_index | host_body_mass_index: 19.5936512638069 |
| SAMN09781680 | collection_date | 2013-01/2014-05 | R3 | 0.70 | paper.fulltext.methods | Samples were collected between January 2013 and May 2014 |
| SAMN09781680 | country | MG | R1 | 0.90 | biosample_attr | Madagascar |
| SAMN09781680 | health_condition | healthy_control | R2 | 0.75 | external.cmd source | disease: Healthy |
| SAMN09781680 | health_condition_detail | Healthy | R2 | 0.75 | external.cmd source | disease: Healthy |
| SAMN09781680 | lifestyle | rural_non_industrialized | R4 | 0.40 | ena.study_title | rural communities from north-eastern Madagascar |
| SAMN09781680 | lifestyle_detail | rural communities of north-eastern Madagascar | R4 | 0.45 | ena.study_description | two rural communities of north-eastern Madagascar |
| SAMN09781680 | sex | male | R2 | 0.75 | external.cmd source | sex: Male |
| SAMN09781681 | subject_id | A05_01_1FE | R1 | 0.85 | biosample.attribute:library_names | A05_01_1FE |
| SAMN09781680 | subject_id | PRJNA485056_A06_01_1FE | R2 | 0.75 | paper.supp.table | Host ID=PRJNA485056_A06_01_1FE |
| SAMN09781684 | timepoint_label | V50 | R1 | 0.70 | run.library_name | V50_01_1FE |
Sequencing
112 runs over 112 samples · mean 5.29 Gbp per run (median 4.56 Gbp, total 592.47 Gbp; 112 runs with a base count) · layout PAIRED 112 · platform ILLUMINA 112 · models Illumina HiSeq 2500 (112) · 86% of runs with a Sandpiper profile · first public 2018-08-10
Authors (80)
Pasolli E first · Asnicar F · Manara S · Zolfo M · Karcher N · Armanini F · Beghini F · Manghi P · Tett A · Ghensi P · Collado MC · Rice BL · DuLong C · Morgan XC · Golden CD · Quince C · Huttenhower C · Segata N last · Tisza MJ first · Buck CB last · Auchtung TA first · Stewart CJ · Smith DP · Triplett EW · Agardh D · Hagopian WA · Ziegler AG · Rewers MJ · She JX · Toppari J · Lernmark Å · Akolkar B · Krischer JP · Vehik K · Auchtung JM · Ajami NJ · Petrosino JF last · Orihara K first · Yahagi K · Saito Y · Watanabe Y · Sasai T · Hara T · Tsukuda N · Oki K · Fujimoto J · Matsuki T last · Hall B first · Levy S · Dufault-Thompson K · Arp G · Zhong A · Ndjite GM · Weiss A · Braccia D · Jenkins C · Grant MR · Abeysinghe S · Yang Y · Jermain MD · Wu CH · Ma B · Jiang X last · Argentini C first · Lugli GA · Tarracchini C · Fontana F · Mancabelli L · Viappiani A · Anzalone R · Angelini L · Alessandri G · Longhi G · Bianchi MG · Taurino G · Bussolati O · Milani C · van Sinderen D · Turroni F · Ventura M last
Downloads
PRJNA485056.csv.gz (5.3 KB) · parquet (77.8 KB) — all 112 samples, every field with route and confidence · PRJNA485056_determinations.csv.gz (14.0 KB) — 1,216 evidence rows