Longitudinal bacterial-fungal microbiome, Spain
143 fecal samples from healthy adults in Spain, studied longitudinally to compare bacterial and fungal (mycobiome) community composition and function, including shotgun metagenomics vs ITS sequencing and correlation with habitual diet. machine-written summary
143 samples · 143 runs · ES · Adult · 2023 · 6.15 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,573 sample values (age, bmi, collection date, country, health condition, health condition detail, latitude, longitude) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC10720197 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| – 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 |
longitudinal
6 of 6 people sampled more than once (143 samples; median 24, up to 24 per person) · follow-up median 49 d (max 53 d) · median interval between samples 7 d (time from collection dates). Schedule stated by the source: “Weekly fecal sample collection per volunteer for 8 weeks (2 months), one sample per week” (time origin: baseline); stated follow-up 56 d.
Each row is one person (6 shown); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 130 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 | 143 | 100% | ||||
| country | 143 | 100% | 143 | |||
| health_condition | 143 | 100% | 143 | |||
| subject_id | 143 | 100% | 143 | |||
| age_at_collection_days | 143 | 100% | 143 | |||
| bmi | 143 | 100% | 143 | |||
| collection_date | 143 | 100% | 143 | |||
| health_condition_detail | 143 | 100% | 143 | |||
| latitude | 143 | 100% | 143 | |||
| longitude | 143 | 100% | 143 | |||
| sex | 143 | 100% | 143 | |||
| timepoint_label | 143 | 100% | 143 |
- Shotgun metagenomics reveals interkingdom association between intestinal bacteria and fungi involving competition for nutrients. 2023 PMID 38098063 PMC10720197 own_data
Archive description
The effect of diet on the composition and function of the bacterial and fungal gut microbiome in a longitudinal setting has not been robustly investigated. Here we first compared two approaches to study the fungal community (Internal-Transcribed-Spacer and shotgun metagenomics), proposed an enrichment protocol to perform a reliable mycobiome analysis, and correlated dietary data with both bacterial and fungal communities. We found that shotgun DNA sequencing after an adapted enrichment fungal protocol provided a cost-effective approach to perform gut mycobiome profiling at the species level and to integrate bacterial and fungal communities in fecal samples. The mycobiome was significantly more dynamic than the bacterial community at the compositional and functional levels. Notably, we showed that microbial diversity, composition, and functions were associated with habitual diet composition instead of driven by global dietary changes. Our study highlights a competitive inter-kingdom interaction between bacteria and fungi for food foraging.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.75. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.title · “healthy human gut microbiome”
- life stage sample.attr.host_age · “24 (n=143/143)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN32809018 | age_at_collection_days | 9131.0 | R1 | 0.85 | sample.attr.host_age | 25 |
| SAMN32809018 | bmi | 17.63 | R1 | 0.90 | sample.attr.host_body_mass_index | 17.63085399 |
| SAMN32809018 | collection_date | 2021-08-13 | R1 | 0.90 | biosample.attribute:collection_date | 2021-08-13 |
| SAMN32809018 | country | ES | R1 | 0.90 | sample.attr.geo_loc_name | Spain |
| SAMN32809018 | health_condition | healthy_control | R1 | 0.90 | biosample_attr | Healthy |
| SAMN32809018 | health_condition_detail | No | R1 | 0.90 | sample.attr.gastrointest_disord | No |
| SAMN32809018 | latitude | 41.4280 | R1 | 0.90 | biosample.attribute:lat_lon | 41.427991 N 2.141921 E |
| SAMN32809018 | longitude | 2.1419 | R1 | 0.90 | biosample.attribute:lat_lon | 41.427991 N 2.141921 E |
| SAMN32809018 | sex | female | R1 | 0.90 | sample.attr.host_sex | female |
| SAMN32809018 | subject_id | L1 | R1 | 0.85 | sample.attr.individual_id | L1 |
| SAMN32809018 | timepoint_label | T1 | R1 | 0.85 | sample.attr.timepoint | T1 |
Sequencing
143 runs over 143 samples · mean 6.45 Gbp per run (median 6.15 Gbp, total 922.41 Gbp; 143 runs with a base count) · layout PAIRED 143 · platform ILLUMINA 143 · models Illumina NovaSeq 6000 (143) · 91% of runs with a Sandpiper profile · first public 2023-07-01
Authors (4)
Xie Z first · Canalda-Baltrons A · d'Enfert C · Manichanh C last
Downloads
PRJNA925700.csv.gz (4.3 KB) · parquet (75.8 KB) — all 143 samples, every field with route and confidence · PRJNA925700_determinations.csv.gz (8.0 KB) — 1,573 evidence rows