Gut Microbiota of Sarawak's "Orang Ulu" Indigenous Community in East Malaysia Reveals Vanish Microbes: A Comparison With Urban Communities

Abstract

Introduction: Urbanization often correlates with reduced diversity in human gut microbiota, with notable variations observed between the gut microbiota among the Indigenous communities in rural villages and urban citizens residing in modern settings. Although research has been conducted on the gut microbiota of healthy adults in Malaysia, there has been no study characterising the gut microbiota of Sarawak's Indigenous communities to date. This study aims to fill this gap by examining the gut microbiota profile of the Sarawak Indigenous groups (specifically Orang Ulu subethnic groups Kayan and Kenyah), comparing them with semi-urbanized Selangor Indigenous communities from Peninsular Malaysia (represented by Proto Malay subtribe Temuan) and Urban communities from Kuala Lumpur.

Methods: We conducted a cross-sectional study and collected stool samples from 86 Indigenous participants from Sarawak and compared them with published data from 45 Malaysian Indigenous participants from Selangor and 18 Urban citizens living in Kuala Lumpur City. DNA was extracted from the stool samples, and subsequently, the V4 hypervariable region of the 16S rRNA gene was sequenced. The raw sequence data were analyzed using the Quantitative Insights into Microbial Ecology 2 (QIIME2) bioinformatics platform.

Results and discussion: Analysis revealed that the Sarawak Indigenous community exhibited the highest gut microbial diversity, followed by the Peninsular Indigenous and Urban groups. The Prevotella/Bacteroides (P/B) ratio revealed that the Sarawak Indigenous community showed the highest presence of Prevotella at 88.3%, while Kuala Lumpur Urban residents had a predominantly Bacteroides composition at 61%. The Selangor Indigenous community also exhibited a Prevotella-dominant profile at 75.5%. VANISH microbes (Prevotella, Faecalibacterium, and Succinivibrio) were identified as dominant genera in the Sarawak Indigenous gut microbiota, contrasting with the BIoSSUM microbe (Bacteroidaceae) found in the Kuala Lumpur cohort.

Conclusion: This study sheds light on the distinct gut microbiota composition of Sarawak's Indigenous community, which has not been previously explored. It highlights the impact of urbanization on gut microbiota composition during lifestyle transitions.

Keywords: 16S rRNA gene sequencing; BloSSUM taxa; Sarawak indigenous; VANISH taxa; gut microbiota.

FIGURE 1

Map for East and West Malaysia and Longhouse in Sarawak at recent times. (A) The map illustrates East Malaysia and West Malaysia, showing the specific sampling locations. For West Malaysia, samples were collected from Kuala Lumpur and Kampung Pangsun in Selangor. In East Malaysia, indigenous stool samples were obtained from Sungai Asap resettlement village, situated in Kapit division, Belaga District, Bintulu, Sarawak. The visualization displays the geographical separation between these sampling regions across Malaysia. (B) The photo represents the longhouse from Sungai Asap in recent times. (Source: These pictures are original pictures and were captured during sample collection for this project in the year 2019).

FIGURE 2

Alpha and Beta diversity of gut microbiota among Sarawak Indigenous, Selangor Indigenous, and Kuala Lumpur Urban Communities. (A,B) Alpha diversity boxplots of species richness and diversity based on their geographical location. A global Kruskal-Wallis test was used for statistical analysis, and a p-value of less than 0.05 (p-value = ≤0.05) was significant. As seen here in the box plots, the alpha diversity measuring indices show significant differences in terms of their location and age categories. (C–E) The figure depicts Principal Coordinates Analysis (PCoA) plots showing gut bacterial beta diversity comparisons among three Malaysian populations. Statistical analysis using Permutational multivariate analysis of variance (PERMANOVA) revealed significant differences in beta diversity based on geographic location, with a p-value of ≤0.05 indicating gut microbial community compositions vary significantly between these populations.

FIGURE 3

The relative abundance bar plots at the genus levels and analysis of the Prevotella/Bacteroides (P/B) ratios. (A) The figure represents the relative abundance (%) of the top 10 taxa identified at the genus level. (B) The figure illustrates the Prevotella/Bacteroides (P/B) ratio across three distinct Malaysian population samples. The Sarawak Indigenous community demonstrated the highest prevalence of Prevotella in their gut. In contrast, the Kuala Lumpur Urban community exhibited a microbiota predominantly characterized by Bacteroides.

FIGURE 4

VANISH and BloSSUM gut microbiota boxplots and Venn diagram of ASVs from Sarawak Indigenous community. (A–E) The figure represents the VANISH and BIoSSUM taxa among the sampled populations. The VANISH taxa are composed of Prevotellaceae, Succinivibrionaceae, and Spirochaetaceae (A–C); the BIoSSUM family taxa are Bacteroidaceae, and Enterobacteriaceae (D,E). A global Kruskal-Wallis test was used for statistical analysis, and a p-value of less than 0.05 (p-value = ≤0.05) was considered to be significant. (F) The figure depicts unique and shared Amplicon Sequence Variants (ASVs) among different communities. 63 and 55 unique ASVs were identified for the Sarawak and Selangor indigenous communities. However, Kuala Lumpur’s urban community revealed the highest number of unique ASV, i.e. 558.

FIGURE 5

MaAsLin2 significant results. (A) This figure represents associations between geographical location (Sarawak and Selangor Indigenous and Kuala Lumpur Urban) and gut microbiota composition at the genus level. Based on significant results, the colour scale bar showed enriched bacteria (red) and reduced bacteria (blue) among the Kuala Lumpur and Selangor communities. (B) Bacterial genera based on their differential abundance among Sarawak Indigenous, Selangor Indigenous, and Kuala Lumpur Urban communities (B–F).