Fig. 1

Variation in the gut microbiome of 650 Malaysians from Orang Asli (OA) villages and Kuala Lumpur (KL). A Violin plots illustrating the percentage of mapped reads with RefSeq (i.e., bacteria, protozoa, fungi, viral, archaea), Unified Human Gastrointestinal Genome (UHGG), and human reference gut microbiome (HRGM) databases between OA (green) and KL (purple) samples. B Relative abundance of phyla from the 237 species of the core gut microbiota of OA and KL populations (left). The relative abundance of the main species from Firmicute A (right). C Bar plot shows the bacterial species that are differentially abundant between Orang Asli and Urban cohort from Kuala Lumpur based on the output of the microbiome multivariable association with linear models 2 (MaAsLin2). The length of the bar corresponds to the value of the significant association. Red color represents the bacterial species associated with the Orang Asli subjects, whereas blue color represents the bacterial species associated with the urban cohort. D The percentage of mapped reads to the HRGM database for samples from different OA villages and KL. E Comparison of pairwise beta diversity at species level within group to the KL cohort, assessed by Jaccard distance based on the distance of nucleotide k-mer sketches k = 21 (top) and genus-level classification (bottom). F Principal coordinates analysis (PCoA) of Jaccard distance based on the gut metagenomic profiles (species levels) in all samples, with individuals from different geographical locations denoted by specific color (ADONIS: p = 0.001, R² = 0.073; ANOSIM: p = 0.001, R = 0.215). The p-values for A, D, and E are computed using Wilcoxon rank-sum test