Gut microbiome/resistome in Orang Asli vs urban Malays, Malaysia
Cross-sectional shotgun metagenomic study of 42 samples from healthy adults across Jahai, Temiar, and Temuan Orang Asli communities and urban Malays in Peninsular Malaysia, comparing gut microbiome and antimicrobial resistance gene profiles. machine-written summary
42 samples · 42 runs · MY · Adult · 2026 · 8.34 Gbp / sample
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what each source gave
| ✓ Sequence archive | 240 sample values (country, health condition, health condition detail, latitude, lifestyle, longitude, sex) |
| ✓ Abstract / description | 84 sample values (location region, 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 |
community — not resolved
42 adults from three Orang Asli communities (Jahai, Temiar, Temuan) and urban Malays; per-sample prefix codes TM/TRk not explained, so no per-sample rows.
Genera, mean relative abundance over 42 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 | 42 | 100% | ||||
| country | 42 | 100% | 42 | |||
| health_condition | 42 | 100% | 42 | |||
| subject_id | 42 | 100% | 42 | |||
| detailed_location | 42 | 100% | ||||
| health_condition_detail | 42 | 100% | 42 | |||
| latitude | 42 | 100% | 42 | |||
| location_region | 42 | 100% | 42 | |||
| longitude | 42 | 100% | 42 | |||
| sex | 21 | 50% | 21 | |||
| lifestyle | 9 | 21% | 9 |
- A framework for gut microbiome and resistome research in Indigenous Orang Asli communities of Peninsular Malaysia 2026 own_data
Archive description
This study presents a comparative shotgun metagenomic analysis of gut microbiome and resistome profiles from 42 healthy adult individuals across three indigenous Orang Asli (OA) communities—Jahai (rural), Temiar (semi-urban), and Temuan (urban)—and urban Malays in Peninsular Malaysia. High-throughput sequencing on the Illumina NovaSeq platform revealed that the rural Jahai exhibited the highest gut microbial diversity, whereas urban Malays showed the lowest. Notably, butyrate-producing genera such as Blautia, Clostridium, and Mediterraneibacter were significantly depleted in the Jahai microbiome. The semi-urban Temiar microbiomes were enriched in Bifidobacterium species. Functional pathway analysis indicated major differences in sugar metabolism and fatty acid biosynthesis pathways, driven largely by microbial compositional shifts. Gut resistome analysis, performed using KMA and ResFinder, showed that urban Temuan and Malay individuals harbored the highest abundance and diversity of antimicrobial resistance genes (ARGs), especially against beta-lactams, tetracyclines, and macrolides. Conversely, the Jahai resistome exhibited the lowest ARG diversity, consistent with reduced antibiotic exposure. These findings highlight the impact of urbanisation on gut microbiome structure and antimicrobial resistance burden, offering valuable insights into microbial transitions in underrepresented Indigenous populations.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.85. Assay shotgun_dna.
- host run.scientific_name · “Homo sapiens”
- body site study.title · “Gut Microbiome and Resistome Diversity”
- life stage study.description · “42 healthy adult individuals”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA118920180 | country | MY | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Malaysia |
| SAMEA118920180 | health_condition | healthy_control | R1 | 0.70 | sample.name_rule:title | J02 |
| SAMEA118920180 | health_condition_detail | Jahai participant, part of '42 healthy adult individuals' cohort | R1 | 0.70 | sample.name_rule:title | J02 |
| SAMEA118920180 | latitude | 4.1093 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 4.10932 109.455475 |
| SAMEA118920192 | lifestyle | urban_industrialized | R1 | 0.70 | sample.name_rule:title | MLY001 |
| SAMEA118920180 | location_region | Peninsular Malaysia | R4 | 0.40 | ena.study_title | Peninsular Malaysia |
| SAMEA118920180 | longitude | 109.4555 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 4.10932 109.455475 |
| SAMEA118920201 | sex | male | R1 | 0.70 | sample.name_rule:title | TM016M |
| SAMEA118920180 | subject_id | SAMEA118920180 | R4 | 0.60 | design.one_sample_per_subject:description | comparative shotgun metagenomic analysis of gut microbiome and resistome profiles from 42 healthy adult individuals |
Sequencing
42 runs over 42 samples · mean 10.11 Gbp per run (median 8.34 Gbp, total 424.60 Gbp; 42 runs with a base count) · layout PAIRED 42 · platform ILLUMINA 42 · models Illumina HiSeq 2000 (42) · 100% of runs with a Sandpiper profile · first public 2026-02-11
Authors (0)
No author record.
Downloads
PRJEB89526.csv.gz (2.1 KB) · parquet (72.1 KB) — all 42 samples, every field with route and confidence · PRJEB89526_determinations.csv.gz (3.2 KB) — 324 evidence rows