Unlike some ecologists who study exotic plants or animals, Dr Christopher van der Gast of the Centre for Ecology & Hydrology is part of a team of ecologists and clinicians working on the bacterial communities that inhabit the lungs of people with CF.

CF is a genetic disorder affecting around 9,000 people in the UK alone. People with CF typically suffer from chronic airways disease caused by bacterial infection, and as 95% of CF sufferers die from respiratory infections, doctors need better ways of treating them.

The traditional medical approach has been to diagnose these lung infections by taking sputum samples from CF patients and looking for a select group of disease-causing bacteria such as Pseudomonas aeruginosa and Staphylococcus aureus by culturing them on agar plates.

While this approach pinpoints the harmful bacteria, it tells clinicians nothing about the dozens of other bacteria that make up the microbial community of the lung. "The traditional approach is to focus on key known pathogens using diagnostic microbiology -- what you can grow on an agar plate. But we cannot grow every bacteria from a given habitat on an agar plate because they all need different growth media," Dr van der Gast explains.

Instead, the team is using ecological models and high-thoughput sequencing to get a complete picture of the bacterial community in the lungs of patients with CF.

They are currently collecting sputum samples from 1,000 CF patients in the UK and US, which are being sequenced by the Wellcome Trust Sanger Institute in Cambridge. This large new study will build on earlier work that has already produced fascinating findings.

The team found for the first time that lung function in CF is linked to microbial diversity -- that paradoxically as lung function worsens, microbial diversity crashes and particular bacteria become dominant -- and that sputum samples from CF patients contain hundreds of species of bacteria in very variable communities.

"As well as the pathogens, we found a surprisingly diverse community of bacteria. The pathogens don't just exist on their own, they are part of complex ecosystem. By using ecological models to identify core species we can help improve treatments for CF patients," he says.

"In order to treat what's there, you have to know what's there and what it's doing. It seems obvious, but it's not been done in the past. We are for the first time treating infectious diseases as ecological communities, not just infections, using ecological insights for clinical benefit."

These ecological insights could also benefit people suffering from other respiratory infections, which the World Health Organization has identified as one of the leading causes of human morbidity and mortality.

According to Dr van der Gast: "Getting a handle on these infections is important for CF patients, but it's also important for people with other lower respiratory tract infections and conditions such as Chronic obstructive pulmonary disease (COPD), which affects more than 1 million people in the UK. Applying ecological approaches may provide fresh insights into many other clinical scenarios."

Dr van der Gast will present his full findings 12:30 on Tuesday 18 December 2012 to the British Ecological Society's Annual Meeting at the University of Birmingham.

His presentation is part of a session on the Ecology and evolution of microbiomes, which includes other papers on CF as well as presentations on microbial communities in human, mouse and bird guts.

According to session organiser Dr Emily Griffiths of the University of Sheffield: "Ecology is all around us, but ecologists are only beginning to study how microbes live within us and other animals. By studying the ecology of the lung and gut, we can begin to understand what makes ecosystems within organisms healthy, and how best to treat certain illnesses.