Indigenous vs non-Indigenous Australian infant gut microbiome
50 gut metagenome samples from Indigenous Australian infants (mostly infants, few neonates) living remotely, compared to age- and sex-matched non-Indigenous urban Australian infants, in a cross-sectional study of early-life microbiome composition. machine-written summary
50 samples · 50 runs · AU · Infant / toddler · 2025 · 1.50 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 100 sample values (collection date, country) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 50 sample values (subject id) · PMC12675544 |
| ✓ Supplementary tables | 150 sample values (age, delivery mode, sex) |
| – 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 49 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 | 50 | 100% | ||||
| country | 50 | 100% | 50 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 50 | 100% | 50 | |||
| age_at_collection_days | 50 | 100% | 50 | |||
| collection_date | 50 | 100% | 50 | |||
| delivery_mode | 50 | 100% | 50 | |||
| sex | 50 | 100% | 50 |
- Indigenous infants in remote Australia retain an ancestral gut microbiome despite encroaching Westernization. PMID 41339319 PMC12675544 curated
Archive description
The gut microbiomes of traditional Indigenous and 'Western' societies differ markedly in diversity and composition. The Western diet modifies the gut microbiome, promoting cardiometabolic disorders that disproportionately affect Indigenous Australians. Studies of Indigenous gut microbiomes are underrepresented in the literature and comparative studies in young children living in traditional and Western societies are lacking, limiting our understanding of early-life microbiome development in different cultural contexts. Therefore, we analyzed gut metagenomes of 50 Indigenous Australian infants (median age < one year) living remotely with variable access to Western foods, compared to age- and sex-matched non-Indigenous infants living in urban Australia. Indigenous infants exhibited greater alpha diversity and significant differences in beta diversity, with 114 species and 38 genera differing in abundance. Some taxa were unique to Indigenous infants, who had higher carriage of Bifidobacteria at younger ages and Prevotella at older ages. In contrast, non-Indigenous infants had a high abundance of Phocaeicola (Bacteroides) across ages. Notably, Indigenous infants had markedly higher numbers of gut viruses and fungi. These findings reveal that despite encroaching Westernization, these Indigenous infants begin life with a gut microbiome that retains key features of traditional societies worldwide. The Western gut microbiome has not been transmitted inter-generationally and has not yet emerged, attesting to the dominant influence of a remote environment and enduring traditional lifestyle. This study provides crucial insights into the early-life microbiome in an Indigenous population and highlights the importance of preserving traditional lifestyles to maintain microbiome diversity.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of infant / toddler and child by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage verdict include”
- body site study.title · “Australian infant gut microbiome metagenomics”
- body site study.description · “The gut microbiomes of traditional”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.title · “Australian infant gut microbiome metagenomics”
- life stage study.description · “studies in young children living in traditional”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA117959966 | age_at_collection_days | 16 | R2 | 0.85 | paper.supp.table | Age_days=16 |
| SAMEA117959966 | collection_date | 2017-01-19 | R1 | 0.85 | biosample.attribute:collection_date | collection_date: 2017-01-19 |
| SAMEA117959966 | country | AU | R1 | 0.90 | biosample_attr | Australia |
| SAMEA117959966 | delivery_mode | vaginal | R2 | 0.85 | paper.supp.table | delivery=V |
| SAMEA117959966 | sex | female | R2 | 0.85 | paper.supp.table | Sex=F |
| SAMEA117959966 | subject_id | SAMEA117959966 | R3 | 0.70 | design.one_sample_per_subject:fulltext | those of 50 age- and sex-matched non-Indigenous infants living in different urban areas of Australia |
Sequencing
50 runs over 50 samples · mean 1.45 Gbp per run (median 1.50 Gbp, total 72.43 Gbp; 50 runs with a base count) · layout SINGLE 50 · platform ILLUMINA 50 · models Illumina NovaSeq 6000 (50) · 98% of runs with a Sandpiper profile · first public 2025-10-06
Authors (20)
Harrison LC first · Allnutt TR · Hanieh S · Roth-Schulze AJ · Ngui KM · Stone NL · Bandala-Sanchez E · Backshell L · Gurruwiwi G · Gondarra V · Couper JJ · Craig ME · Davis EA · Huynh T · Soldatos G · Wentworth JM · Vuillermin P · Penno MAS · Biggs BA · ENDIA Study Group Consortium last
Downloads
PRJEB87209.csv.gz (2.1 KB) · parquet (71.6 KB) — all 50 samples, every field with route and confidence · PRJEB87209_determinations.csv.gz (3.0 KB) — 300 evidence rows