Gut Microbiome in Helminth-Infected Indigenous Malaysians
650 longitudinal gut metagenome samples from indigenous Malaysians across 5 villages with varying soil-transmitted helminth infection prevalence, studying effects of helminth status and albendazole anthelmintic treatment on the microbiome. machine-written summary
650 samples · 650 runs · MY · Adult · 2022 · 3.01 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 8,679 sample values (antibiotic exposure, country, health condition, health condition detail, intervention, intervention detail, latitude, lifestyle) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC12246136, PMC13079874, PMC9727879, PMC9790084 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 1,474 sample values (age, antibiotic exposure, health condition, health condition detail) · from curatedMetagenomicData 3 (cMD 3) |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
intervention · arms resolved
132 people have samples in more than one arm.
Non-antibiotic pharmaceutical given as the study intervention (metformin design single_arm_before_after · population gi_infection_or_diarrhoea · Albendazole anthelmintic treatment (deworming), longitudinal pre/post sampling
“Longitudinal changes in the microbiome in response to albendazole anthelmintic treatment” — abstract:36476263 (study level; per-sample arms are in the intervention column below)
longitudinal — not resolvedcommunity
132 of 407 people sampled more than once (375 samples; median 3, up to 3 per person). Schedule stated by the source: “fecal sample pre-treatment, then 21 and 42 days after albendazole treatment” (time origin: intervention_start); stated follow-up 42 d.
Orang Asli from 5 villages (Bangkong 47, Judah 116, Legong 100, Rasau 48, Tanjung_Sepat 40 subjects); KL urban controls without village unit5 shared settings.
member · circles are people (pale = no sequenced sample), arrows run donor → recipient and parent → child, curved lines join twins, partners and siblings, squares are shared settings or families without recorded roles. Shown: 5 shared settings. 407 people in the project overall.
Genera, mean relative abundance over 598 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 | 650 | 100% | ||||
| country | 650 | 100% | 650 | |||
| health_condition | 650 | 100% | 298 | 352 | ||
| subject_id | 650 | 100% | 650 | |||
| detailed_location | 650 | 100% | ||||
| health_condition_detail | 650 | 100% | 298 | 352 | ||
| intervention | 650 | 100% | 650 | |||
| intervention_detail | 650 | 100% | 650 | |||
| latitude | 650 | 100% | 650 | |||
| lifestyle | 650 | 100% | 650 | |||
| location_locality | 650 | 100% | 650 | |||
| location_region | 650 | 100% | 650 | |||
| longitude | 650 | 100% | 650 | |||
| sex | 650 | 100% | 650 | |||
| age_at_collection_days | 634 | 98% | 634 | |||
| shared_setting_id | 594 | 91% | 594 | |||
| shared_setting_type | 594 | 91% | 594 | |||
| antibiotic_exposure | 280 | 43% | 144 | 136 | ||
| timepoint_label | 251 | 39% | 251 |
- Clostridia isolated from helminth-colonized humans promote the life cycle of Trichuris species. 2022 PMID 36450245 PMC9790084 own_data
- Gut microbiome of helminth-infected indigenous Malaysians is context dependent. 2022 PMID 36476263 PMC9727879 own_data
- Global diversity of soil-transmitted helminths reveals population-biased genetic variation that impacts diagnostic targets. 2025 PMID 40640199 PMC12246136 own_data
- Comprehensive benchmarking of metagenomic binning tools reveals key factors for improved genome recovery. 2026 PMID 41980943 PMC13079874 unsure
Archive description
While microbiomes in industrialized societies are well characterized, indigenous populations with traditional lifestyles have microbiomes that are more akin to those of ancient humans. However, metagenomic data in these populations remains scarce and the association with soil-transmitted helminth infection status is unclear. Here, we sequenced 650 metagenomes of indigenous Malaysians from 5 villages with different prevalence of helminth infections. Individuals from villages with higher prevalence of helminth infections have more unmapped reads and greater microbial diversity. Microbial community diversity and composition were most strongly associated with different villages and the effects of helminth infection status on the microbiome varies by village. Longitudinal changes in the microbiome in response to albendazole anthelmintic treatment was observed in both helminth infected and uninfected individuals. Inference of bacterial population replication rates from origin of replication analysis identified specific replicating taxa associated with helminth infection. Our results indicated that helminth effects on the microbiota was highly dependent on context and effects of albendazole on the microbiota can be confounding for the interpretation of deworming studies. Furthermore, a substantial quantity of the microbiome remains undescribed and this large dataset from indigenous populations associated with helminth infections should facilitate characterization of the disappearing microbiome from developed industrialized societies.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult and child by sonnet_x2 with confidence 0.75. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site run.scientific_name · “human gut metagenome”
- life stage sample.attr.age_group · “18 and above (n=425/650)”
- life stage sample.attr.age_group · “12 and below (n=204/650)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN25042866 | age_at_collection_days | 15705.75 | R2 | 0.75 | external.cmd source | age: 43; age_unit: Year; age_group: Adult |
| SAMN25042869 | antibiotic_exposure | no | R1 | 0.90 | biosample_attr | No |
| SAMN25042882 | antibiotic_exposure | no | R2 | 0.75 | external.cmd source | antibiotics_current_use: No |
| SAMN25042866 | country | MY | R1 | 0.90 | sample.attr.geo_loc_name | Malaysia |
| SAMN25042866 | health_condition | other_infection | R1 | 0.85 | biosample.attribute:helminth | helminth: Yes |
| SAMN25042867 | health_condition | healthy_control | R2 | 0.75 | external.cmd source | disease: Healthy |
| SAMN25042866 | health_condition_detail | soil-transmitted helminth infection (helminth=Yes) | R1 | 0.85 | biosample.attribute:helminth | helminth: Yes |
| SAMN25042867 | health_condition_detail | Healthy | R2 | 0.75 | external.cmd source | disease: Healthy |
| SAMN25042866 | intervention | no_intervention | R1 | 0.80 | biosample.attribute:Subject_timepoint | Subject_timepoint: KR004B_Pre |
| SAMN25042867 | intervention | drug_therapy | R1 | 0.80 | biosample.attribute:group | group: Indigenous_people_Post 1 |
| SAMN25042866 | intervention_detail | baseline before deworming treatment | R1 | 0.80 | biosample.attribute:Subject_timepoint | Subject_timepoint: KR004B_Pre |
| SAMN25042867 | intervention_detail | first follow-up after anthelmintic deworming treatment | R1 | 0.80 | biosample.attribute:group | group: Indigenous_people_Post 1 |
| SAMN25042866 | latitude | 3.8500 | R1 | 0.90 | biosample.attribute:lat_lon | 3.85 N 101.45 E |
| SAMN25042866 | lifestyle | indigenous_community | R1 | 0.85 | biosample.attribute:group | group: Indigenous_people_Pre |
| SAMN25042866 | location_locality | Rasau | R1 | 0.85 | biosample.attribute:village | Rasau |
| SAMN25042866 | location_region | Perak | R1 | 0.85 | biosample.attribute:states | Perak |
| SAMN25043460 | location_region | Kuala Lumpur | R1 | 0.60 | biosample.attribute:lat_lon | 3.12 N 101.65 E |
| SAMN25042866 | longitude | 101.4500 | R1 | 0.90 | biosample.attribute:lat_lon | 3.85 N 101.45 E |
| SAMN25042866 | sex | female | R1 | 0.90 | sample.attr.gender | female |
| SAMN25042866 | shared_setting_id | Rasau | R1 | 0.85 | biosample.attribute:Village | Village: Rasau |
| SAMN25042866 | shared_setting_type | village_or_community | R1 | 0.85 | biosample.attribute:Village | Village: Rasau |
| SAMN25042866 | subject_id | KR004B | R1 | 0.70 | sample.name_rule:Subject_timepoint | KR004B_Pre |
| SAMN25042866 | timepoint_label | Pre | R1 | 0.70 | sample.name_rule:group | Indigenous_people_Pre |
Sequencing
650 runs over 650 samples · mean 3.08 Gbp per run (median 3.01 Gbp, total 2,003.93 Gbp; 650 runs with a base count) · layout PAIRED 650 · platform ILLUMINA 650 · models Illumina NovaSeq 6000 (650) · 92% of runs with a Sandpiper profile · first public 2022-01-22
Authors (80)
Sargsian S first · Chen Z · Lee SC · Robertson A · Thur RS · Sproch J · Devlin JC · Tee MZ · Er YX · Copin R · Heguy A · Pironti A · Torres VJ · Ruggles KV · Lim YAL · Bethony J · Loke P · Cadwell K last · Easton AV · Yap NJ · Lee IL · Devlin J · Ng KS · Subramanian P · Angelova A · Oyesola O · Ngui R · Beiting DP · Boey CCM · Chua KH · Papaiakovou M first · Waeschenbach A · Ajibola O · Ajjampur SS · Anderson RM · Bailey R · Benjamin-Chung J · Cambra-Pellejà M · Caro NR · Chaima D · Cimino RO · Cools P · Cossa A · Dunn J · Galagan S · Gandasegui J · Grau-Pujol B · Houlder EL · Ibikounlé M · Jenkins TP · Kalua K · Kjetland EF · Krolewiecki AJ · Levecke B · Luty AJ · MacDonald AS · Mandomando I · Manuel M · Martínez-Valladares M · Mejia R · Mekonnen Z · Messa A · Mpairwe H · Muchisse O · Muñoz J · Mwinzi P · Novela V · Odiere MR · Sacoor C · Walson JL · Williams SA · Witek-McManus S · Littlewood DTJ · Cantacessi C · Doyle SR last · Kim J first · Kim N · Cha JH · Ma J · Lee I last
Downloads
PRJNA797994.csv.gz (21.5 KB) · parquet (100.6 KB) — all 650 samples, every field with route and confidence · PRJNA797994_determinations.csv.gz (91.2 KB) — 10,153 evidence rows