Population level biomarkers of gut health in commercial flocks

University of New England

  • Project code: PRJ-011908

  • Project stage: Closed

  • Project start date: Sunday, June 30, 2019

  • Project completion date: Thursday, June 24, 2021

  • Journal Articles From Project: Microbial taxa in dust and excreta associated with the productive performance of commercial meat chicken flocks Animal Microbiome (Issue: under revision on 24/5/2021), Molecular detection of Eimeria species and Clostridium perfringens in poultry dust and pooled excreta of commercial broiler chicken flocks differing in productive performance Veterinary Parasitology (Issue: 291 on 3/1/2021)

  • National Priority: CME-Priority 3-Contributing to efficient and secure chicken production systems


Robust and practical biomarkers to assess gut health and important gut pathogens at a population level would provide a valuable tool for industry and research. It could be used to ensure widespread and rational implementation and evaluation of disease prevention strategies and a reduction in the therapeutic use of antibiotics. This project will assess the usefulness of population level monitoring of necrotic enteritis and coccidiosis based on molecular testing of dust samples. Preliminary data collected during experimental trials at UNE show that dust testing enables discrimination between flocks with and without the causative agent of necrotic enteritis (NE) and preliminary screening of end of batch dust samples indicates a relatively low prevalence of infection with Clostridium perfringens carrying the netB gene. This needs wider evaluation under field conditions, including potential associations with performance. We will systematically investigate population level biomarkers for gut health using dust samples and faeces to differentiate flocks with good and poor production performance. The research would provide a clear determination of the potential of dust and faeces analysis to predict flock health status. Findings from this work will have important implications for managing flock health by providing applied tools for assessing disease status, particularly sub-clinical disease where few or no practical tools currently exist.


Chicken Meat

Research Organisation

University of New England

Objective Summary

The broad objective of this project is to evaluate and identify practical and affordable candidate biomarkers for flock gut health by investigating the following specific questions:

a. Is dust testing useful to monitor or predict clinical and subclinical NE?

b. Is dust testing useful to monitor the level of coccidiosis challenge?

c. What are the microbiota profiles in non-invasive population level samples such as dust and faeces and can these provide a signature that correlates with good or poor flock performance?

The major outcome from this work will be the determination of whether testing of population level samples provides a practical, affordable and useful research or management tool to monitor

  1. Important microbiota disruptors such as C. perfringens and coccidia and,
  2. Gut health more broadly as assessed by dust and pooled faecal microbiota, which will potentially provide a tool to monitor gut health and/or evaluate management interventions.

The project will incorporate 2 strands of work that will be performed using the same data set. In consultation with industry collaborators Cordina and Baiada, the top 10 and bottom 10 farms in terms of performance (feed conversion ratio) will be selected for longitudinal studies. Dust samples will be collected using settle plates and faeces samples collected from the floor weekly and production data will be recorded.

  1. Gut pathogen detection. The usefulness of dust samples combined with PCR as a diagnostic tool to monitor NE
    (Clostridium perfringens and the netB gene) and coccidia (Eimeria maxima, E. acervulina, E. tenella, and E. brunetti) will be evaluated.
  2. Gut health markers. Dust and faeces samples will be subjected to high throughput DNA sequencing of 16S ribosomal RNA gene amplicons and the microbial profile of each sample will be determined. These results will be correlated to the production data collected to identify possible relationships between bacterial communities and performance.