Equol producer vs non-producer gut metagenomes in Spain
Cross-sectional shotgun metagenome study of 5 faecal samples from healthy adult women in Spain, comparing equol producers (n=3) and non-producers (n=2) to examine gut microbiota composition and function linked to equol production. machine-written summary
5 samples · 5 runs · ES · Adult · 2023 · 5.53 Gbp / sample
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what each source gave
| ✓ Sequence archive | 25 sample values (collection date, country, latitude, location region, longitude) |
| ✓ Abstract / description | 15 sample values (health condition, health condition detail, subject id) |
| – Full text | no open-access full text linked |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – 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 |
Genera, mean relative abundance over 3 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 | 5 | 100% | ||||
| country | 5 | 100% | 5 | |||
| health_condition | 5 | 100% | 5 | |||
| subject_id | 5 | 100% | 5 | |||
| collection_date | 5 | 100% | 5 | |||
| detailed_location | 5 | 100% | ||||
| health_condition_detail | 5 | 100% | 5 | |||
| latitude | 5 | 100% | 5 | |||
| location_region | 5 | 100% | 5 | |||
| longitude | 5 | 100% | 5 |
- Assessment of short-read shotgun sequencing and microbiome analysis of faecal samples to discriminate between equol producers and non-producers. 2023 PMID 37078124 own_data
Archive description
Among the isoflavones and isoflavone-derived metabolites, equol, which in the human gut is synthesized from daidzein by minority bacterial populations, shows the strongest estrogenic and antioxidant activity. The beneficial effects on human health of isoflavone consumption might be partially or indeed totally attributable to this equol. Although some of the bacterial strains involved in its formation have been identified, the interplay between the composition and functionality of the gut microbiota and equol producer phenotype has hardly been studied. In this study, three analytical pipelines for the taxonomic and functional annotation of shotgun sequencing data were used in the search for similarities and differences in the faecal metagenome of equol producer (n=3) and non-producer (n=2) women, with special focus on equol-producing taxa and their equol-associated genes. The taxonomic profiles of the faecal samples differed significantly depending on the analytical method followed, although the microbial diversity detected by each tool was very similar at the phylum, genus and species levels. In addition, equol-producing taxa were detected in both equol producer and non-producer women, but no correlation between the abundance of equol-producing taxa and the equol producer/non-producer phenotype was found. Indeed, functional metagenomic analysis was unable to identify the pathways and genes involved in equol production, even in samples from equol producers. By aligning the reductase-encoding genes involved in equol production with the collected metagenomics data, only two reads mapping to daidzein- and tetrahydrodaidzein-reductase sequences were recognized in a sample from an equol producer. In conclusion, the taxonomic analysis of metagenomic data might not be suitable for detecting and quantifying equol-producing microbes in human faeces. Functional analysis of the data might provide an alternative. However, to detect the genetic makeup of the minority gut populations, more extensive sequencing than that contemplated in the present study might be required.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.65. Assay shotgun_dna.
- host study.description · “faecal metagenome of equol producer”
- body site study.description · “faecal metagenome of equol producer”
- life stage study.description · “equol producer (n=3) and non-producer (n=2) women”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA110164431 | collection_date | 2017 | R1 | 0.90 | biosample.attribute:collection_date | 2017 |
| SAMEA110164431 | country | ES | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Spain |
| SAMEA110164431 | health_condition | healthy_control | R4 | 0.40 | study.title | Equol producers and non-producers |
| SAMEA110164431 | health_condition_detail | equol producer vs non-producer phenotype; healthy volunteers in dietary/metabolite study | R4 | 0.40 | study.title | Equol producers and non-producers |
| SAMEA110164431 | latitude | 43.3666 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 43.3666200 -5.8611200 |
| SAMEA110164431 | location_region | Asturias | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 43.3666200 -5.8611200 |
| SAMEA110164431 | longitude | -5.8611 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 43.3666200 -5.8611200 |
| SAMEA110164431 | subject_id | SAMEA110164431 | R4 | 0.60 | design.one_sample_per_subject:abstract | faecal metagenome of equol-producing (n=3) and non-producing (n=2) women |
Sequencing
5 runs over 5 samples · mean 5.62 Gbp per run (median 5.53 Gbp, total 28.11 Gbp; 5 runs with a base count) · layout PAIRED 5 · platform ILLUMINA 5 · models Illumina HiSeq 1000 (5) · 60% of runs with a Sandpiper profile · first public 2023-06-02
Authors (0)
No author record.
Downloads
PRJEB53649.csv.gz (1.1 KB) · parquet (70.5 KB) — all 5 samples, every field with route and confidence · PRJEB53649_determinations.csv.gz (1.1 KB) — 40 evidence rows