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

Abstract

BackgroundMicrobiome 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. This limits our understanding of human-host microbiota interactions in their broadest sense. Here we examined the airway microbiology of the Orang Asli, the indigenous peoples of Malaysia. In addition to exploring the carriage and antimicrobial resistance of important respiratory pathobionts, we also present the first investigation of the nasal microbiomes of these indigenous peoples, in addition to their oral microbiomes.ResultsA total of 130 participants were recruited to the study from Kampung Sungai Pergam and Kampung Berua, both sites in the north-eastern state of Terengganu in Peninsular Malaysia. 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 non-vaccine type 23A (14.6%) and the vaccine type 6B (9.8%). The nasal microbiome was significantly more diverse in those aged 5-17 years compared to 50+ years (p = 0.023). In addition, samples clustered by age (PERMANOVA analysis of the Bray-Curtis distance, p = 0.001). Hierarchical clustering of Bray-Curtis dissimilarity scores revealed six microbiome types. The largest cluster (n=28; 35.4%) had a marked abundance of Corynebacterium.Others comprised Corynebacterium with Dolosigranulum, two clusters were definable by the presence of Moraxella, one with and the other without Haemophilus, a small grouping of Delftia/ Ochrobactum profiles and one with Streptococcus. No Staphylococcus profiles were observed. In the oral microbiomes Streptococcus, Neisseria and Haemophilus were dominant. Lower levels of Prevotella, Rothia, Porphyromonas, Veillonella and Aggregatibacter were also among the eight most observed genera.ConclusionsWe present the first study of Orang Asli airway microbiomes and pathobiont microbiology. Key findings include the prevalence of pneumococcal serotypes that would be covered by pneumococcal conjugate vaccines if introduced into a Malaysian national immunisation schedule, and the high level of S. aureus carriage. The dominance of Corynebacterium in the airway microbiomes is particularly intriguing given its’ consideration as a potentially protective commensal with respect to acute infection and respiratory health.