Dataset Information

The upper respiratory tract microbiome of indigenous Orang Asli in north-eastern Peninsular Malaysia.

ABSTRACT: Much microbiome research has focused on populations that are predominantly of European descent, and from narrow demographics that do not capture the socio-economic and lifestyle differences which impact human health. Here we examined the airway microbiomes of the Orang Asli, the indigenous peoples of Malaysia. A total of 130 participants were recruited from two sites in the north-eastern state of Terengganu in Peninsular Malaysia. Using 16S rRNA sequencing, the nasal microbiome was significantly more diverse in those aged 5-17 years compared to 50+ years (p?=?0.023) and clustered by age (PERMANOVA analysis of the Bray-Curtis distance, p?=?0.001). Hierarchical clustering of Bray-Curtis dissimilarity scores revealed six microbiome clusters. The largest cluster (n?=?28; 35.4%) had a marked abundance of Corynebacterium. In the oral microbiomes Streptococcus, Neisseria and Haemophilus were dominant. Using conventional microbiology, high levels of Staphylococcus aureus carriage were observed, particularly in the 18-65 age group (n?=?17/36; 47.2% 95% CI: 30.9-63.5). The highest carriage of pneumococci was in the <5 and 5 to 17 year olds, with 57.1% (4/7) and 49.2% (30/61), respectively. Sixteen pneumococcal serotypes were identified, the most common being the nonvaccine-type 23A (14.6%) and the vaccine-type 6B (9.8%). The prevalence of pneumococcal serotypes covered by pneumococcal conjugate vaccines support introduction into a Malaysian national immunisation schedule. In addition, the dominance of Corynebacterium in the airway microbiomes is intriguing given their role as a potentially protective commensal with respect to acute infection and respiratory health.

SUBMITTER: Cleary DW

PROVIDER: S-EPMC7785749 | biostudies-literature | 2021 Jan

REPOSITORIES: biostudies-literature

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The upper respiratory tract microbiome of indigenous Orang Asli in north-eastern Peninsular Malaysia.

Cleary David W DW Morris Denise E DE Anderson Rebecca A RA Jones Jessica J Alattraqchi Ahmed Ghazi AG A Rahman Nor Iza NI Ismail Salwani S Razali Mohd Sayuti MS Mohd Amin Rahmah R Abd Aziz Aniza A Esa Nor Kamaruzaman NK Amiruddin Salman S Chew Ching Hoong CH Simin Hafis H Abdullah Ramle R Yeo Chew Chieng CC Clarke Stuart C SC

NPJ biofilms and microbiomes 20210105 1

Much microbiome research has focused on populations that are predominantly of European descent, and from narrow demographics that do not capture the socio-economic and lifestyle differences which impact human health. Here we examined the airway microbiomes of the Orang Asli, the indigenous peoples of Malaysia. A total of 130 participants were recruited from two sites in the north-eastern state of Terengganu in Peninsular Malaysia. Using 16S rRNA sequencing, the nasal microbiome was significantly ...[more]

PMID: 33402693

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Project description:BACKGROUND:Recent advances in genomic technologies have facilitated genome-wide investigation of human genetic variations. However, most efforts have focused on the major populations, yet trio genomes of indigenous populations from Southeast Asia have been under-investigated. RESULTS:We analyzed the whole-genome deep sequencing data (~ 30×) of five native trios from Peninsular Malaysia and North Borneo, and characterized the genomic variants, including single nucleotide variants (SNVs), small insertions and deletions (indels) and copy number variants (CNVs). We discovered approximately 6.9 million SNVs, 1.2 million indels, and 9000 CNVs in the 15 samples, of which 2.7% SNVs, 2.3% indels and 22% CNVs were novel, implying the insufficient coverage of population diversity in existing databases. We identified a higher proportion of novel variants in the Orang Asli (OA) samples, i.e., the indigenous people from Peninsular Malaysia, than that of the North Bornean (NB) samples, likely due to more complex demographic history and long-time isolation of the OA groups. We used the pedigree information to identify de novo variants and estimated the autosomal mutation rates to be 0.81 × 10- 8 - 1.33 × 10- 8, 1.0 × 10- 9 - 2.9 × 10- 9, and ~ 0.001 per site per generation for SNVs, indels, and CNVs, respectively. The trio-genomes also allowed for haplotype phasing with high accuracy, which serves as references to the future genomic studies of OA and NB populations. In addition, high-frequency inherited CNVs specific to OA or NB were identified. One example is a 50-kb duplication in DEFA1B detected only in the Negrito trios, implying plausible effects on host defense against the exposure of diverse microbial in tropical rainforest environment of these hunter-gatherers. The CNVs shared between OA and NB groups were much fewer than those specific to each group. Nevertheless, we identified a 142-kb duplication in AMY1A in all the 15 samples, and this gene is associated with the high-starch diet. Moreover, novel insertions shared with archaic hominids were identified in our samples. CONCLUSION:Our study presents a full catalogue of the genome variants of the native Malaysian populations, which is a complement of the genome diversity in Southeast Asians. It implies specific population history of the native inhabitants, and demonstrated the necessity of more genome sequencing efforts on the multi-ethnic native groups of Malaysia and Southeast Asia.

Project description:BackgroundDengue is prevalent among Malaysia's indigenous peoples, known as the Orang Asli, and it poses a serious health threat to them. The study aims to look at the socio-demographic factors, health beliefs, and knowledge about dengue and its association to dengue prevention practices among Orang Asli communities in Peninsular Malaysia.MethodsA cross-sectional survey was conducted in 16 randomly selected Orang Asli villages from eight states in Peninsular Malaysia from April 2012 until February 2013.ResultsA total of 560 Orang Asli were interviewed and 505 completed the survey. Slightly above half of the participants (n = 280, 55.4%) had a total dengue prevention score of 51-100 (of a possible score of 0-100). Multivariate analysis findings showed dengue knowledge, perceived barriers to perform dengue prevention, fogging frequency, and perceived susceptibility to dengue fever as significant factors associated to dengue prevention practices. Participants with a lower dengue knowledge score (score 0-18) were less likely (OR = 0.63, 95%CI = 0.44-0.92 vs. score 19-36, P = 0.015) to practice dengue prevention. Participants with low perceived barriers to prevent dengue (score of 1-5) were more likely (OR = 2.06, 95%CI = 1.21-3.53, vs. score of 6-10, P = 0.008) to practice dengue prevention. Villages that were not fogged (OR = 0.49, 95%CI = 0.24-0.99, P = 0.045) or rarely fogged (OR = 0.40, 95%CI = 0.22-0.75, P = 0.004) had lower dengue prevention practices than villages that were fogged often. Participants with low perceived susceptibility of acquiring dengue (score of 1-5) were less likely (OR = 0.54, 95%CI = 0.33-0.89 vs. score of 6-10, P = 0.018) to practice dengue prevention measures.ConclusionFindings imply that educational and health programmes should focus on enhancing dengue knowledge and perceived susceptibility of acquiring dengue and reducing perceived barriers to performing dengue prevention practices among the Orang Asli. More outreach on mosquito control campaigns should be carried out especially in villages where mosquito fogging is frequent.

Project description:BackgroundGiardia duodenalis is a flagellate parasite which has been considered the most common protozoa infecting human worldwide. Molecular characterization of G. duodenalis isolates have revealed the existence of eight groups (Assemblage A to H) which differ in their host distribution. Assemblages A and B are found in humans and in many other mammals.MethodsThis cross-sectional study was conducted to identify assemblage's related risk factors of G. duodenalis among Orang Asli in Malaysia. Stool samples were collected from 611 individuals aged between 2 and 74 years old of whom 266 were males and 345 were females. Socioeconomic data were collected through a pre-tested questionnaire. All stool samples were processed with formalin-ether sedimentation and Wheatley's trichrome staining techniques for the primary identification of G. duodenalis. Molecular identification was carried out by the amplification of a triosephosphate isomerase gene using nested-PCR assay.ResultsSixty-two samples (10.2%) were identified as assemblage A and 36 (5.9%) were assemblage B. Risk analysis based on the detected assemblages using univariate and logistic regression analyses identified subjects who have close contact with household pets i.e. dogs and cats (OR = 2.60; 95% CI = 1.42, 4.78; P = 0.002) was found to be significant predictor for assemblage A. On the other hand, there were three significant risk factors caused by assemblage B: (i) children ≤15 years old (OR = 2.33; 95% CI = 1.11, 4.87; P = 0.025), (ii) consuming raw vegetables (OR = 2.82; 95% CI = 1.27, 6.26; P = 0.011) and (iii) the presence of other family members infected with giardiasis (OR = 6.31; 95% CI = 2.99, 13.31; P < 0.001).ConclusionsThe present study highlighted that G. duodenalis infection among Orang Asli was caused by both assemblages with significant high prevalence of assemblage A. Therefore, taking precaution after having contact with household pets and their stool, screening and treating infected individuals, awareness on the importance of good health practices and washing vegetables are the practical intervention ways in preventing giardiasis in Orang Asli community.

Dataset Information

The upper respiratory tract microbiome of indigenous Orang Asli in north-eastern Peninsular Malaysia.

Publications

The upper respiratory tract microbiome of indigenous Orang Asli in north-eastern Peninsular Malaysia.

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