PHD international: Understanding the calf health and welfare in commercial farms through digital approaches

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INRAE presentation

The French National Research Institute for Agriculture, Food, and Environment (INRAE) is a major player in research and innovation. It is a community of 12,000 people with 272 research, experimental research, and support units located in 18 regional centres throughout France. Internationally, INRAE is among the top research organisations in the agricultural and food sciences, plant and animal sciences, as well as in ecology and environmental science. It is the world’s leading research organisation specialising in agriculture, food and the environment. INRAE’s goal is to be a key player in the transitions necessary to address major global challenges. Faced with a growing world population, climate change, resource scarcity, and declining biodiversity, the Institute has a major role to play in building solutions and supporting the necessary acceleration of agricultural, food and environmental transitions.

Work environment, missions and activities

Presentation of the professional environment

The activity will take place within the Joint Research Unit Interactions Hôtes–Agents Pathogènes (UMR IHAP), located on the campus of the National Veterinary School of Toulouse (ENVT). Affiliated with the Animal Health Department of INRAE, UMR IHAP is a multidisciplinary research structure in animal infectiology that brings together a large community of researchers, engineers, technicians, and support staff, organized into 7 scientific teams and 2 support teams dedicated to management and animal experimentation.

Its objective is to understand the complex interactions that develop between pathogenic microorganisms and their hosts at different scales of biological organization (molecule – cell – individual – population), with the ultimate goal of proposing innovative control methods. The research covers a wide range of infectious agents (viruses, bacteria, parasites, and prions) that affect the well‑being, health, and performance of numerous animal species and hosts.

Objectives of the position

This PhD project aims to enhance the sustainability of cattle production systems by developing innovative approaches to assess and protect calf health and welfare under real commercial conditions. Using precision livestock farming technologies, the student will analyse behavioural patterns, microphone‑based acoustic signals (including AI‑driven cough detection), and physiological sensor data such as accelerometers and ruminal boluses.

Description of the tasks to be carried out or tasks to be performed

The main points of the PhD thesis will be :

1. Identify early, non‑invasive indicators of calf welfare

Develop behavioural, acoustic, and physiological markers that reliably signal pain, discomfort, disease onset, or resilience in commercial

farming conditions.

2. Analyse behavioural patterns associated with health and welfare trajectories

Use continuous behavioural monitoring (e.g., activity, posture, social interactions) to characterise how calves respond to respiratory and

digestive challenges.

3. Develop AI‑based acoustic models for welfare assessment

Process and classify microphone data—particularly coughs and distress‑related vocalisations—using machine learning to detect early

signs of illness or compromised welfare.

4. Integrate digital sensor data into welfare phenotyping

Combine information from accelerometers, ruminal boluses, and other precision livestock farming tools to build multidimensional welfare

profiles.

5. Link welfare indicators to sustainable production outcomes

Evaluate how early welfare signals relate to antibiotic use, growth performance, resilience, and overall sustainability of cattle production

systems.

6. Contribute to decision‑support tools for farmers

Translate research findings into practical, field‑ready indicators that help farmers monitor welfare, intervene earlier, and improve the

sustainability and ethical standards of their operations.

Relationship Field of the Job

The project is intrinsically international, both in its scientific design and in its operational implementation. It is carried out within a large, multi‑country consortium that brings together leading institutions across Europe and beyond, including INRAE and ENVT (France), IRTA, CSIC and UAB (Spain), UNITUS (Italy), Wageningen University (Netherlands), Aarhus University (Denmark), and La Salle University (Spain). This network ensures a rich exchange of expertise in microbiology, immunology, animal behavior, bioacoustics, digital farming, and structural biology. All partners have already reviewed and approved the experimental protocol, guaranteeing methodological coherence and shared scientific standards across countries.

 

The first phase of the thesis will take place in a fully equipped commercial farm located in Lleida, Spain, which has already been validated by the consortium for its suitability, safety standards, and operational capacity. This industrial‑scale facility houses more than 10,000 animals and offers the infrastructure required to conduct longitudinal research under real farming conditions while ensuring the safety of both animals and personnel. The farm is equipped with secure containment systems specifically designed for handling large animals, including robust restraint cages, protected handling corridors, and dedicated spaces for biological sampling. These systems allow safe manipulation of calves and adult cattle during procedures such as blood collection, nasal swabs, and fecal sampling. After completing the experimental phase, the student will spend some months at IRTA (Monells, Spain) and at ENVT in Toulouse, France.

Training and skills

Master/Ingénieur (Bac+5)

• Proficiency in scientific English.
• The ideal candidate has a strong background in animal science, biology, ethology, or related fields, with a clear interest in animal welfare and innovative digital farming approaches.
• Experience or interest in digital breeding technologies (accelerometers, ruminal bolus, microphones).
• Curious, rigorous, and comfortable working both in controlled research settings and commercial farms.
• A genuine motivation for sustainability and ethical livestock production is essential, along with the ability to collaborate within an international consortium.
• Skills in data analysis, statistics, or modelling (R, Python, or similar).
• Experience or interest in precision livestock technologies (accelerometers, ruminal boluses, microphones).
• Ability to work with behavioral and acoustic data.
• Understanding of multidisciplinary approaches (health, microbiota, behavior, environment).
• Ability to work in an international team and to communicate science (written/oral).
• Autonomy, critical sense, organization and motivation to conduct a longitudinal follow-up in breeding.

INRAE's life quality

By joining our teams, you benefit from (depending on the type of contract and its duration):

- up to 30 days of annual leave + 15 days "Reduction of Working Time" (for a full time);
- parenting support: CESU childcare, leisure services;
- skills development systems: training, career advise;
- social support: advice and listening, social assistance and loans;
- holiday and leisure services: holiday vouchers, accommodation at preferential rates;
- sports and cultural activities;
- collective catering.

How to apply

To apply, go to the ADUM website (https://adum.fr/as/ed/voirproposition.pl?matricule_prop=72589&site=adumR) and follow the instructions provided.

A l’attention de Núria Mach : nuria.mach@inrae.fr  and Antonio Velarde : Antonio.velarde@irta.cat

Date limite de dépôt des candidatures : 31/05/2026.