Charting Changes in the Respiratory Microbiome

Even with the widespread use of vaccines, respiratory tract infections continue to contribute significantly to global morbidity and mortality and cause millions of deaths every year. Sadly, the burden of this often falls on young children and the elderly. In regions of the world where vaccines aren’t part of a national schedule, understanding the true impact of respiratory infections is vital to informing good policy decisions and determining the most effective vaccine implementation strategy for the future.

To understand how to improve respiratory tract health, researchers have been exploring its microbiome, which spans from the inside of the nose down to the lungs. From our first screaming introduction into the world, this microbiome is shaped by our environment, and early exposures affect us long term.

We know, for example, that certain compositions of bacteria are linked to the development of chronic respiratory diseases, such as asthma. We also know that these compositions can change over the first few years of life and are heavily influenced by our surroundings. Living with siblings, residing in the rolling countryside vs. a concrete jungle, or attending daycare – where the tsunami of snot signals a lifestyle well beyond the sharing of toys – each can have a significant impact on your microbiota.

Then, of course, there are the bacteria that cause disease that call our airways home. The Dr. Jekyll of this world is Streptococcus pneumoniae. While most strains of pnuemococci behave quite innocuously, a few are Hyde-like and can cause meningitis and pneumonia, with potentially deadly consequences. It is by no means the only two-faced villain; Haemophilus influenzae and Staphylococcus aureus can also cause serious illness.  

To balance this, many members of the microbial consortia have potentially protective qualities. These bacteria seem to prevent the carriage of pathogens in ways we are just beginning to understand. The potential for targeting these interactions to reduce disease is clear and could yield alternative approaches to treatment.

Our research focuses on Malaysia, a country where the pneumococcal vaccine is not freely available. It is thought that the risk of respiratory epidemics or pandemics is particularly high in South East Asia, where the emergence of novel infectious diseases is likely to be associated with increased urbanization and climate change. If that were not reason enough to focus here, the indiscriminate distribution of antibiotics does nothing to prevent our march towards an apocalyptic post-antibiotic world.

My most recent work includes collaborators Dr. Stuart Clarke from the University of Southampton and Professor Dr. Yeo Chew Chieng from Universiti Sultan Zainal Abidin (UniSZA). With support from uBiome’s grant program and a Newton Fund Institutional Links award from the British Council, we visited Orang Asli tribes (literally translated as “the first people”) in Terengganu State, Northeast Malaysia.

Pockets within these communities are becoming increasingly westernized as a consequence of tourism, employment in the palm oil industry, or migration to larger urban areas. We already know, from others’ work with groups that live traditional lifestyles, that the microbiomes of these peoples have shown fascinating differences compared to western populations. For example, populations of hunter-gatherers from Tanzania and the Peruvian Amazon, as well as agriculturist communities in Burkina Faso, Malawi, Venezuela, and the Andean highlands, have greater bacterial diversity, and consequently functionality, in oral and gut microbiomes. They also experience greater populations of particular Genera, such as Prevotella.

Our goals from this work are simple. We want to see how common it is to carry disease-causing bacteria, and identify how the composition of the respiratory microbiome correlates with this in these unique populations. This latter point is important because if we aim to modify the microbiome – whether to encourage the outgrowth of protective species or to minimize the carriage of pathogens – the first step must be to get a more complete understanding of this body site. Ultimately, we hope that the partnerships we have developed with the local Orang Asli tribes will help us reduce the local and regional burden of infectious disease.   

Dr. Cleary is a Senior Research Fellow in Microbial Sciences at the NIHR Southampton Biomedical Research Centre and Faculty of Medicine, University of Southampton. He is the recipient of a uBiome grant to research the respiratory tract microbiome in Malaysian communities. You can connect with him on Twitter.