IndoMEE: Gut Microbiome Relative Abundance Across Indonesian and Singaporean Populations

Indonesian Microbiome Ecology and Evolution (IndoMEE) version 1 database catalogues species-level reference genomes assembled from gut metagenomes of 116 human individuals from 8 communities across the Indonesian archipelago, representing hunter-gatherer, agricultural, and urban lifestyles. The dataset contains relative abundance of these genomes across the 116 Indonesians and 109 Singaporeans analyzed in a 2025 Cell Reports study. It was authored by Clarissa Febinia and is shared under a CC-BY-4.0 license.

Use Cases

• Compare gut microbiome composition between hunter-gatherer, agricultural, and urban lifestyles based on the described sample collection.
• Analyze species-level genomic diversity across the Indonesian archipelago based on the 8 sampled communities.
• Investigate the social microbiome shaping over rural-to-urban transitions referenced in the associated study.
• Benchmark metagenomic assembly and analysis methods using the catalogue of 116 reference genomes.

Strengths

• Includes data from 225 individuals (116 Indonesians and 109 Singaporeans).
• Samples represent a range of lifestyles from 8 distinct communities across Indonesia.
• Associated with a peer-reviewed 2025 publication in Cell Reports.

Limitations

• Column-level documentation is absent; field semantics must be inferred after download.
• Row count is unknown, which may limit suitability assessment.
• Data may reflect geographic bias inherent to the specific 8 Indonesian communities sampled.

Provenance

Source

figshare, authored by CLARISSA FEBINIA.

Collection Method

Species-level reference genomes (MAGs) assembled from short-read gut metagenomes.

Freshness

Last updated 2026-05-10 20:37:56; freshness should be verified.

Geography

8 communities across the Indonesian archipelago and Singapore.