Human-gut microbiota codiversification across populations
Cross-sectional study of 2750 gut metagenome samples from paired human genome/microbiome individuals across Europe, Asia and Africa, including mothers and children, examining codiversification between host and gut microbiota. machine-written summary
2,750 samples · 2,750 runs · VN, GA, DE · Infant / toddler · 2022 · 0.31 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 2,668 sample values (subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC11019788, PMC11494892, PMC12688249 |
| ✓ Supplementary tables | 8,560 sample values (age, country, health condition, health condition detail, sex) |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinalmother–infant — not resolved
900 of 900 people sampled more than once (2,658 samples; median 3, up to 10 per person) · follow-up median 7 d (max 10 d) · median interval between samples 7 d (time from age at collection).
Each row is one person (36 shown of 900); dots are samples at days since that person's first sample.
Cohort of 1,225 people incl. mothers and their children (Suzuki 2022); per-sample mother–child linkage not in archive metadata.
Genera, mean relative abundance over 2,161 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 | 2,049 | 75% | ||||
| country | 2,081 | 76% | 2,081 | |||
| health_condition | 1,763 | 64% | 1,763 | |||
| subject_id | 2,658 | 97% | 2,658 | |||
| age_at_collection_days | 2,049 | 75% | 2,049 | |||
| health_condition_detail | 1,763 | 64% | 1,763 | |||
| sex | 904 | 33% | 904 | |||
| timepoint_label | 10 | 0% | 10 |
- Taxonomic and metabolic development of the human gut microbiome across life stages: a worldwide metagenomic investigation. PMID 38441032 PMC11019788 curated
- Exploring the vitamin biosynthesis landscape of the human gut microbiota. PMID 39287373 PMC11494892 curated
- Infection with gut parasites correlates with gut microbiome diversity across human populations in Africa. PMID 41358671 PMC12688249 curated
Archive description
The gut microbiomes of human populations worldwide have many core microbial species in common. However, within a species, some strains can show remarkable population specificity. The question is whether such specificity arises from a shared evolutionary history (codiversification) between humans and their microbes. To test for codiversification of host and microbiota, we analyzed paired gut metagenomes and human genomes for 1225 individuals in Europe, Asia and Africa, including mothers and children. Between and within countries, a parallel evolutionary history was evident for humans and their gut microbes. Moreover, species displaying the strongest codiversification independently evolved traits characteristic of host dependency, including reduced genomes, and oxygen and temperature sensitivity. These findings all point to the importance of understanding the potential role of population-specific microbial strains in microbiome-mediated disease phenotypes. Please note: 1) Metagenomes with the same study ID, but different “_X” appendages, where X is an integer, are technical replicates of the same biological sample (which were aggregated before using in the study). 2) The number of reads reported in the manuscript's supplement are less than that reflected in the ENA metadata this is because the former are post-QC read counts, and the latter are raw sequencing read counts.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of infant / toddler and child and adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage verdict include”
- body site study.title · “Codiversification of gut microbiota with humans”
- body site study.description · “The gut microbiomes of human”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.description · “including mothers and children . Between and”
- life stage study.description · “and Africa, including mothers and children. Between”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA111355071 | age_at_collection_days | 10958.0 | R2 | 0.85 | paper.supp.msystems.00929-24-s0003.xlsx[Table S1!Age (years)] | ERR10207278: 30 |
| SAMEA111355071 | country | VN | R2 | 0.75 | paper.supp.table | Geographic origin=Vietnam |
| SAMEA111355071 | health_condition | healthy_control | R2 | 0.85 | paper.supp.msystems.00929-24-s0003.xlsx[Table S1!Disease] | ERR10207278: NO |
| SAMEA111355071 | health_condition_detail | NO | R2 | 0.85 | paper.supp.msystems.00929-24-s0003.xlsx[Table S1!Disease] | ERR10207278: NO |
| SAMEA111355105 | sex | female | R2 | 0.85 | paper.supp.table | sex=F |
| SAMEA111355069 | subject_id | V238 | R1 | 0.70 | sample.name_rule:alias | V238_1 |
| SAMEA111407927 | timepoint_label | D12 | R1 | 0.70 | sample.title | S1919_plate1_D12 |
Sequencing
2,750 runs over 2,750 samples · mean 0.50 Gbp per run (median 0.31 Gbp, total 1,371.15 Gbp; 2,750 runs with a base count) · layout PAIRED 2,750 · platform ILLUMINA 2,750 · models Illumina HiSeq 3000 (2,750) · 79% of runs with a Sandpiper profile · first public 2022-09-16 – 2022-09-29
Authors (31)
Mancabelli L first · Milani C · De Biase R · Bocchio F · Fontana F · Lugli GA · Alessandri G · Tarracchini C · Viappiani A · De Conto F · Nouvenne A · Ticinesi A · Bussolati O · Meschi T · Cecchi R · Turroni F · Ventura M last · van Sinderen D · Ngwese MM first · Adegbite BR · Zinsou JF · Fitzstevens JL · Schmidt VT · Moure PAN · Maloum MN · Tyakht AV · Huus KE · Youngblut ND · Kremsner PG · Adegnika AA · Ley RE last
Downloads
PRJEB46788.csv.gz (71.5 KB) · parquet (192.5 KB) — all 2,750 samples, every field with route and confidence · PRJEB46788_determinations.csv.gz (133.8 KB) — 11,228 evidence rows