Home » Research » PhD Research Programme » Complex systems & Metagenomics » Tracking and tackling goat farm-associated pneumonia using a metagenomics approach

Tracking and tackling goat farm-associated pneumonia using a metagenomics approach

This project is part of the overarching project 'DiSSeMINATE - Drivers of Selection and Spread of Mobile Genetic Elements INvolved in Antimicrobial Resistance'.


2019 - 2023

Group and collaboration

Collaboration: Wim van der Poel (Wageningen University & Research (WU & WVBR)), Alex Bossers (WUR-WBVR / UU-IRAS), Marcel Hulst (WUR-WBVR), Thomas Hagenaars (WUR-WBVR)

PhD student: Wouter Lokhorst

Project description

In the Netherlands, an increased incidence of community-acquired pneumonia near goat farms has been reported, possibly due to bioaerosols. Currently, there is no clear link to one or more causative agent due to a lack of knowledge on the temporal and spatial patterns of goat farm microbiota and the health effects they have on their environment. The proposed research attempts to obtain more knowledge about this, using both a metagenomics and a One Health approach.

A primary objective will be to identify molecular signatures of pathogens or ultimately the agent or agents that cause goat-related community-acquired pneumonia in humans. It features multiple sampling sites per goat farm, which will be sampled multiple times per year. This accurately determines the contribution of each potential source to goat farm microbial transmissions within the farm and emissions from the farm through metagenomics.

The relationship between farm management practices and the presence of zoonotic pathogens will then be studied using machine learning methods. Intervention strategies can be developed and their effectiveness evaluated using the metagenomics methods. Especially if a pathogen is found in the parallel research project directed at pneumonia in nearby residents.

Successful development of the methods used here will lead to reduced zoonotic potential of goat farms and allows for usability of these methods in other monitoring or experimental setups on various scales, e.g. similar approaches could be applied to livestock farms of other species.


  • Proposal writing
  • Sampling
  • Lab work
  • Data analysis
  • Report writing

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: ‘I feel like an explorer’

Goat farms may specifically host pneumonia-causing micro-organisms. Wouter Lokhorst identifies microbes on these farms to obtain a better insight into causative agents of pneumonia.