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.
Highlights
Much microbiome research has, to-date, been focused on populations that are predominantly of European descent, and from demographics that do not capture the socio-economic and lifestyle challenges which impact human health[1]
For example children of Warao communities in Venezuela have been shown to be at increased risk of pneumococcal disease[10], and it is well established that Aboriginal infants are highly susceptible to otitis media caused by Non-typeable Haemophilus influenzae (NTHi)[11]
As a site that can be colonised by commensals, as well as opportunistic pathogens such as the pneumococcus[21], S. aureus[22] and H. influenzae[23], understanding the microbiology of the upper respiratory tract is key in tackling respiratory disease
Summary
To-date, been focused on populations that are predominantly of European descent, and from demographics that do not capture the socio-economic and lifestyle challenges which impact human health[1]. The study of non-Western, unindustrialised populations is an important extension of microbiome research so that we may understand human host–microbiota interactions in their broadest sense. There remains a paucity of data regarding microbiomes of other anatomical sites of the upper respiratory tract (URT). This lack of data requires addressing given the evidence that geographically isolated and/or indigenous populations endure distinct burdens of respiratory infections. With respiratory infectious diseases continuing to be a significant component of global morbidity and mortality[12], the interest in the microbiome of the upper airways stems from its’ importance in an individual’s susceptibility to respiratory infection, in part through the presence of resilient taxa which prevent colonisation and/or outgrowth of specific pathobionts[13]. To date no study has undertaken a comprehensive analysis of the URT microbiome of the indigenous populations of Peninsular Malaysia, the Orang Asli
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