Gut microbiome bile acid metabolism in centenarians
Cross-sectional study of 330 gut microbiome samples from elderly and adult subjects (country not collected), examining bacteria that generate secondary bile acids, including isoalloLCA, with antimicrobial effects against multidrug-resistant pathogens. machine-written summary
330 samples · 330 runs · JP · Elderly · 2021 · 1.75 Gbp / sample · cohort Age-dependent changes in the gut microbiota and se
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,120 sample values (age, health condition, health condition detail, sex, subject id) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 330 sample values (country) · PMC10726799, PMC11364081, PMC11367760, PMC11488730, PMC11559365, PMC11865343, PMC12604771 |
| ✓ Supplementary tables | 350 sample values (health condition, health condition detail) |
| – 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 — not resolved
20 of 307 people sampled more than once (41 samples; median 2, up to 3 per person).
Genera, mean relative abundance over 306 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 | 330 | 100% | ||||
| country | 330 | 100% | 330 | |||
| health_condition | 328 | 99% | 154 | 174 | ||
| subject_id | 328 | 99% | 328 | |||
| health_condition_detail | 330 | 100% | 154 | 176 | ||
| sex | 330 | 100% | 330 | |||
| age_at_collection_days | 154 | 47% | 154 |
- Novel bile acid biosynthetic pathways are enriched in the microbiome of centenarians. 2021 PMID 34325466 own_data
- Age-dependent changes in the gut microbiota and serum metabolome correlate with renal function and human aging. 2023 PMID 38015106 PMC10726799 own_data
- Enteropathway: the metabolic pathway database for the human gut microbiota. 2024 PMID 39222063 PMC11367760 own_data
- EasyMetagenome: A user-friendly and flexible pipeline for shotgun metagenomic analysis in microbiome research. 2025 PMID 40027489 PMC11865343 own_data
- Consistent signatures in the human gut microbiome of longevous populations. 2024 PMID 39197040 PMC11364081 unsure
4 more
- Comprehensive gut microbiota composition and microbial interactions among the three age groups. 2024 PMID 39423213 PMC11488730
- Biosynthetic potential of the gut microbiome in longevous populations. 2024 PMID 39529240 PMC11559365
- Chemical modulation of gut bacterial metabolism induces colanic acid and extends the lifespan of nematode and mammalian hosts. 2025 PMID 41218018 PMC12604771
- Examination of shared gut microbiome signatures in aging and Parkinson's disease. 2026 PMID 41907847 PMC13021664
Archive description
Centenarians, who are living more than a century, represent the ultimate model of successful longevity associated with less susceptibility to aging-associated illness and chronic inflammation. The gut microbiota has been considered as a criticial determinant for human health and longevity. Here we show that centenarians (average 107 yo) have distinct gut microbiome enriched in microbes capable of generating unique secondary bile acids, include iso-,3-oxo, and iso-allo-lithocolic acid (LCA), as compared to elderly (85-89 yo) and young (21-55 yo) controls. In particular, iso-allo-LCA biosysnthesis pathway had not been defined. By screening of 68 bacterial isolates from a centenarian's faecal microbiota, we identified Paraceteroides merdae and Odoribacteraceae stains as effective producers of iso-all-LCA. Furthermore, we revealed that 5'-reductase (5AR) and 3'-hydroxysteroid dehydrogenase (3'HSDH) were responsible for the iso-allo-LCA generation by generating and testing mutant P. merdae strains. Iso-allo-LCA exerted the most potent antimicrobial effects among the test bile acid compounds, against gram-positive (but not gram-negative) multidrug-resistant pathogens, such as Clostridium difficile and vancomycin-resitant Enterococcus faecium. These findings suggest that specific bile acid metabolism may be involved in reducing the risk of acquiring pathobionts and their related diseases, thereby potentially contributing to longevity.
How this project entered the registry
Classified as human blood / tissue / internal fluids / gut / stool shotgun DNA metagenome of elderly and adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_unknown_no_evidence”
- body site study.title · “Identification of unique bile acid metabolizing bacteria”
- body site study.description · “generating unique secondary bile acids, include iso-,3-oxo,”
- body site study.description · “chronic inflammation. The gut microbiota has been”
- life stage study.title · “the microbiome of centenarians”
- life stage study.description · “Centenarians , who are”
- life stage sample.attr.age · “22 (n=44/330)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN20081612 | age_at_collection_days | 32469.0 | R1 | 0.85 | sample.attr.age | 89 |
| SAMN20081612 | country | JP | R3 | 0.70 | paper.fulltext.methods | Japan aging datasets were retrieved via the public database |
| SAMN20081612 | health_condition | healthy_control | R1 | 0.80 | biosample_attr | Elderly_control |
| SAMN20081722 | health_condition | healthy_control | R2 | 0.80 | paper.supp.ACEL-22-e14028-s002.xlsx[Supplementary Table 1!Group] | IF_001: Group=Centenarian |
| SAMN20081612 | health_condition_detail | Elderly_control | R1 | 0.85 | biosample.attribute:category | category: Elderly_control |
| SAMN20081722 | health_condition_detail | Centenarian | R2 | 0.85 | paper.supp.ACEL-22-e14028-s002.xlsx[Supplementary Table 1!Group] | Centenarian |
| SAMN20081612 | sex | female | R1 | 0.90 | sample.attr.gender | female |
| SAMN20081612 | subject_id | KWS_10452 | R1 | 0.70 | sample.name_rule:library_name | KWS_10452 |
Sequencing
330 runs over 330 samples · mean 1.98 Gbp per run (median 1.75 Gbp, total 652.75 Gbp; 330 runs with a base count) · layout PAIRED 330 · platform ILLUMINA 330 · models Illumina NovaSeq 6000 (330) · 93% of runs with a Sandpiper profile · first public 2021-08-25
Authors (175)
Sato Y first · Atarashi K · Plichta DR · Arai Y · Sasajima S · Kearney SM · Suda W · Takeshita K · Sasaki T · Okamoto S · Skelly AN · Okamura Y · Vlamakis H · Li Y · Tanoue T · Takei H · Nittono H · Narushima S · Irie J · Itoh H · Moriya K · Sugiura Y · Suematsu M · Moritoki N · Shibata S · Littman DR · Fischbach MA · Uwamino Y · Inoue T · Honda A · Hattori M · Murai T · Xavier RJ · Hirose N · Honda K last · Shiroma H first · Darzi Y · Terajima E · Nakagawa Z · Tsuchikura H · Tsukuda N · Moriya Y · Okuda S · Goto S · Yamada T last · Ma J first · Yang X · He J last · Bai D first · Chen T · Xun J · Ma C · Luo H · Yang H · Cao C · Cao X · Cui J · Deng YP · Deng Z · Dong W · Du J · Fang Q · Fang W · Fang Y · Fu F · Fu M · Fu YT · Gao H · Ge J · Gong Q · Gu L · Guo P · Guo Y · Hai T · Liu H · He ZY · Hou H · Huang C · Ji S · Jiang C · Jiang GL · Jiang L · Jin LN · Kan Y · Kang D · Kou J · Lam KL · Li C · Li F · Li L · Li M · Li X · Li ZT · Liang J · Lin Y · Liu C · Liu D · Liu F · Liu J · Liu T · Liu X · Liu Y · Liu B · Liu M · Lou W · Luan Y · Luo Y · Lv H · Ma T · Mai Z · Mo J · Niu D · Pan Z · Qi H · Shi Z · Song C · Sun F · Sun Y · Tian S · Wan X · Wang G · Wang H · Wang J · Wang K · Wang L · Wang SK · Wang X · Wang Y · Xiao Z · Xing H · Xu Y · Yan SY · Yang L · Yang S · Yang Y · Yao X · Yousuf S · Yu H · Lei Y · Yuan Z · Zeng M · Zhang C · Zhang H · Zhang J · Zhang N · Zhang T · Zhang YB · Zhang Y · Zhang Z · Zhou M · Zhou Y · Zhu C · Zhu L · Zhu Y · Zhu Z · Zou H · Zuo A · Wen T · Chen S · Li G · Gao Y · Liu YX last · Hu G first · Savini M · Cooke MB · Wei X · Deng D · Gao SM · Xia RA · Guan Y · Wen AX · Yu X · Herman C · Li J · Wang MC last
Downloads
PRJNA675598.csv.gz (9.5 KB) · parquet (83.5 KB) — all 330 samples, every field with route and confidence · PRJNA675598_determinations.csv.gz (12.3 KB) — 1,800 evidence rows