PhD position: Microbiota-host interactions associated with the regulation of methane emissions and feed efficiency in ruminants

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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

You will work within the Herbivores Joint Research Unit. This unit’s mission is to generate, integrate, and disseminate knowledge, and to share expertise in order to design multi-functional herbivore livestock systems that address the challenges of global change (environmental, socioeconomic, and the digital transition). The unit has 118 permanent staff members and hosts 70 non-permanent staff members each year. It is organized into four research teams, a management team, and a support team. You will work within the DINAMIC team (Digestion, Nutrition, Absorption, and Microbes), which conducts research on the microbial digestion of animal feed and nutrient absorption, a critical component of research in animal feed and nutrition.

Thesis Project Summary

Reducing enteric methane emissions in cattle is a major challenge for the sustainability of livestock systems. Indeed, methane is a potent greenhouse gas. However, methane is naturally produced by the ruminal microbiota during feed fermentation. The microbiota also plays a major role in the animal feed efficiency by converting the feed consumed into nutrients that the animal can utilize. Consequently, feed efficiency is theoretically associated with methane production, as the energy from feed that is lost as methane is no longer available to the animal. Thus, the hypothesis that the inhibition of methane production would enhance feed efficiency is compelling. However, this hypothesis is currently being contested as experimental studies do not consistently demonstrate enhanced performance when methane production is inhibited (Morgavi et al. 2023). In some cases, adverse effects on digestibility and feed efficiency have even been observed (Hu et al. 2026).

A recent meta-analysis of studies on dairy cows has shown that the specific inhibition of methane production—methanogenesis—can lead to reduced feed intake and milk production, as well as altered milk composition (Martins et al. 2025). For example, the concentration of urea in milk increases, which could indicate an overall decrease in the animal’s nitrogen use efficiency and, by extension, changes in nitrogen metabolism. At the ruminal level, the inhibition of methanogenesis is generally associated with a change in the composition of the microbiota. The proportion of methanogens tends to decrease, while the composition of bacteria following inhibition varies across studies (Ungerfeld and Pitta, 2025). From a metabolic perspective, the inhibition of methanogenesis leads to an accumulation of dihydrogen and a redirection of the synthesis pathways for volatile fatty acids—the primary energy sources for ruminants, toward propionate synthesis (Cao et al. 2025; Hu et al. 2026). Some studies also show increases in methylated compounds and branched-chain volatile fatty acids in the rumen following the inhibition of methanogenesis (Martinez-Fernandez et al. 2018, 2016). However, the changes reported in the literature at the ruminal level are not sufficient to explain the aforementioned physiological changes.

Thus, the ruminal microbiota appears to be the key factor determining the trade-off between methane emissions and animal performance, but its role, depending on experimental conditions, remains to be clarified. 

The objective of this thesis is therefore to determine how changes in the composition and activity of the ruminal microbiota, induced by the addition of anti-methane supplements to feed rations, modulate the dynamic balance between methane emissions and feed efficiency in cattle.

This thesis is based on three experiments conducted as part of the Methane2030 project:

• a first experiment conducted on 48 dairy cows supplemented with two complementary anti-methane supplements, in total, five paired rumen fluid and blood samplings were performed on all cows during this trial;
• a second experiment was conducted on 40 finishing beef cattle that were supplemented with an anti-methane supplement, in total, three paired rumen fluid and blood samples were collected from all the finishing beef cattle during this trial;
• a third experiment was conducted on 48 heifers supplemented with an anti-methane supplement from birth, in total, 5 paired rumen fluid and blood samples were collected from all calves during this trial.

Candidate perspective

Your mission will be to study the changes in the ruminal microbiota induced by the use of anti-methane supplements and to investigate their associations with the animal metabolism and feed efficiency in dairy cows and finishing beef cattle.

You will focus specifically on demonstrating changes in the composition and functions of methanogens as well as bacterial populations involved in protein degradation before, during, and after the use of anti-methane supplements. 

You will rely on two complementary approaches to characterize the interactions between the ruminal microbiota and the host. First, metagenomic and metatranscriptomic sequencing of the ruminal microbiota to track changes in the microbiota composition and functional activity. Second, metabolomic analysis of plasma and rumen samples to detect variations in host responses over time as well as potential drivers of these responses at the ruminal level. All data will be integrated and statistically analyzed using multivariate approaches and predictive models to link microbial and metabolic changes to measures of animal performance and methane emissions. 

Specifically, you will be responsible for:

1. conducting a literature review on the links between ruminal microbiota metabolism and host metabolism within the general context outlined above, in order to structure your thesis research question;
2. defining a strategy for selecting samples to be analyzed based on available physiological data, in accordance with the chosen hypotheses;
3. generating and analyzing omics data on the rumen microbiota and metabolic data from the host, integrate this data with physiological data to identify mechanisms potentially associated with responses to anti-methane supplementation;
4. disseminating research findings through scientific publications and oral presentations at scientific conferences.

Training and skills

Academic background: Bac+5 in microbiology, biochemical analysis, or molecular biology.

Professional experience: Previous experience in a research laboratory is preferred.

Scientific knowledge and technical skills:

• understanding of the ruminal ecosystem and its role in host nutrition;
• knowledge of omics data analysis;
• practical laboratory skills, particularly in sample preparation.

Personal and interpersonal skills:

• ability to work collaboratively within a multidisciplinary team;
• strong interest and enthusiasm for scientific research;
• ability to synthesize and critically analyze scientific information;
• excellent scientific writing and communication skills.

INRAE's life quality

By joining INRAE, you can benefit from, depending on the type and duration of your contract:

- up to 30 days of annual leave + up to 15 additional days off (for full-time employees);
- access to the French public healthcare system;
- 50% of the cost of your supplementary health insurance covered by INRAE;
- childcare and parenting support;
- training and career guidance;
- social assistance and financial support;
- holiday vouchers and accommodation at preferential rates;
- sports and cultural activities;
- subsidised staff restaurants.

The Theix site located in Saint-Genès-Champanelle is served by the T2C bus line number P39 as well as a demand transport line, it is also equipped with parking and services dedicated to cycling.

How to apply

I send my CV and my motivation letter