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Metagenomic analysis of animal, environmental and human microbiomes in the context of excess pneumonia risk around livestock production farms in the Netherlands: flow of microorganisms

Group and collaboration

Marion Koopmans & Matt Cotton (Department of Viroscience, Erasmus MC), Dick Heederik & Lidwien Smit (IRAS,UU) Debby Bogaert (UMCU) Arjan Stegeman (DGK, UU) Collaboration: BVM WUR Lelystad (Alex Bossers), RIVM and others.
PhD student: Kirsty Kwok

Project description

In recent year, an increased risk of pneumonia for residents living near farms has been implicated. In 2007-2010, the largest Dutch Q-fever epidemic with more than 4000 cases has been reported and was associated with local dairy goat and sheep farms. These alarming evidences emphasize the importance of one health and investigating the health effects from exposure of livestock farms, thus measures can be implemented to reduce any public health risks at the human-animal interface.

Here, we aim to investigate the risk of pneumonia due to farm-related exposures. We hypothesize that the excess pneumonia risk results from either inhalation of potentially farm-related pathogens, or, alternatively, farm-related exposures may lead to changes in the composition and diversity of the upper respiratory tract microbiome and virome that results in increased pneumonia risk through dysbiosis. We aim to characterize the livestock farm metagenome (both microbiome and virome) by performing metagenomic sequencing in livestock samples, respiratory samples from people with farm-related exposures and farm dust (environmental samples) and then relate the metagenomes with farm management practices and characteristics. Subsequently, we will measure and model movement of microbes and viruses to exposed neighboring residents using existing emission models and refine these approaches by combining measurements and modeling. Meanwhile, we will perform a systematic assessment to study the etiologies of pneumonia in residents living near intensive farming areas in the Netherlands so as to estimate the pneumonia risk from farm-related exposures. By integrating geo-spatial and molecular epidemiological concepts, we ultimately aim to create regional maps for describing concentrations of selected relevant microbial pollutants to facilitate identification of high-risk populations under normal operational circumstances and during animal disease outbreaks.

Collectively, this study would provide a better understanding of the flow of microbes between the (farm-) environment, livestock and the human airway and the underlying mechanisms of livestock-related respiratory health risks. This study would also guide science-based preventive initiatives using health impact scenario studies under one health approach and improve preparedness in case of zoonotic disease outbreaks.


Complex Systems & Metagenomics is the overarching theme for more than 10 PhD tracks in NCOH projects to create new interdisciplinary, inter-thematic, and inter-institutional research collaborations.

PhD student interview

Interview: Exploring the flow of viruses at the human-animal-environment interface: Towards One Health Preparedness

‘During 2007-2010, there was a huge Q-fever outbreak with more than four thousand cases in the Netherlands, that was originated from dairy goat and sheep farms. Further investigation of infectious disease at animal-human interface is warranted. Follow-up epidemiological studies observed an excess pneumonia risk in residents living close to farms, however the mechanisms behind remain... More