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2020-2023

Improving resistance to colonisation of the gut microbiota by vancomycin-resistant enterococci: proof of concept of a preclinical model in the mouse and determination of the underlying mechanisms

• PhD student: Alan JAN
• Supervisor: Lionel RIGOTTIER-GOIS (MICALIS, Département MICA)
• Cofunding: 50% INRAE / 50% ED ABIES (AgroParisTech)

The gastrointestinal tract is a reservoir for opportunistic pathogenic agents, or pathobionts, which benefit from an imbalance of the gut microbiota (dysbiosis) to proliferate in predisposed patients. Vancomycin-resistant enterococci (VRE) arise from the gastrointestinal tract where their proliferation precedes their dissemination via the blood and lymphatic circulation and then infection. Understanding the mechanisms responsible for resistance to intestinal colonisation by VRE is essential to fighting infections and limiting the spread of antibiotic resistance. Recent studies have demonstrated the efficacy of using commensal bacteria as a strategy to enhance resistance to colonisation of the gut microbiota by enterococci. This project aims to elucidate the mechanism(s) for resistance to enterococcal colonisation using commensal bacterial in a preclinical mouse model. To achieve this goal, we shall combine high-throughput sequencing techniques, mathematical modelling and modelling of the microbial ecology of gut microbiota dynamics in a mouse model. The knowledge acquired will enable us to propose commensal bacteria as an alternative or supplement to antibiotics, and as markers for the risk of proliferation of pathobionts induced by antibiotics.

2019-2022

Systemic understanding of microbial interactions and ruminal fermentation

• PhD student: Ibrahim FAKIH
• Supervisors: Rafael MUNOZ-TAMAYO (MOSAR, Département PHASE), Evelyne Forano (MEDIS, Département MICA)
• Cofunding: 50% INRAE / 50% Lallemand Animal Nutrition

The microbiota of the rumen plays an essential role in ruminant nutrition by degrading and fermenting feed, thus transforming it into a source of energy and proteins for the host. In order to optimise these functions, it is necessary to determine the mechanisms involved and to be able to predict the effect of biotic or abiotic factors on the structure and activity of this complex ecosystem. The development of omic approaches has enabled description of the composition of the ruminal microbiota, its genomic potential and its activity with respect to certain targeted functions. However, we still do not know how to precisely describe the function of the ecosystem at the level of the microbiota, to optimise its functioning in the long term or to predict its evolution following different disturbances. With this goal in mind, mathematical modelling offers a powerful tool to better understand the functioning of the ruminal ecosystem. The PhD project aims to improve our understanding of rumen functioning at the systemic scale by developing a multidisciplinary approach that integrates the characterisation of microbial metabolism using omic approaches and the development of models at the genomic scale of bacteria in the rumen. Microbial interactions will be studied in vitro under a “bottom-up” synthetic ecology approach using mini consortia composed of key rumen micro-organisms representing the principal functions of this ecosystem (cellulolysis, amylolysis, proteolysis, methanogenesis) whose genomes are known. The mini consortia tested will be of increasing complexity and supplemented by the yeast Saccharomyces cerevisiae in order to model the effect on microbial activities of this probiotic when used as an additive in animal nutrition.

2019-2022

Epithelial chymotrypsin: impact on the host-gut microbial biofilm interface

• PhD student: Simon GUIGNARD
• Supervisors: Chrystelle BONNART, Nathalie VERGNOLLE (IRSD, Département MICA)
• Cofunding: 50% INRAE / 30% INSERM / 20% Université de Calgary

Proteases have different physiological functions that are important to maintaining our digestive health. Chymotrypsin (CTR) is a pancreatic protease that appears to fulfil extra-pancreatic functions. Indeed, our findings have indicated an important epithelial source in the human and mouse intestine (small intestine and colon). Chymotrypsin may therefore play an important role in the interface between the epithelium and the microbiota. In the context of a PhD project, we are proposing the theory that intestinal epithelial chymotrypsin may exert both autocrine control on epithelial cells and a paracrine effect on the architecture of the intestinal microbial biofilm. We have already demonstrated the ability of this enzyme to activate intra-epithelial MAPK-type signalling and calcium mobilisation by cleaving the PAR epithelial receptor. Study of the effects of this activation on the biology of epithelial cells, and on the intestinal barrier, will form part of the objectives of this PhD project. During preliminary work, we have shown that host proteases are able to modify the physical and biological characteristics of the intestinal microbial biofilm. Another question will therefore be to establish whether chymotrypsin might affect the structure and functions of the intestinal microbial biofilm. According to data in the literature, anti-inflammatory properties have been attributed to chymotrypsin, but no study has demonstrated these effects in a context of intestinal inflammation. We will determine whether the administration of chymotrypsin can improve the state of the digestive mucosa and its bacterial biofilm in mouse models of intestinal inflammation. This research should throw new light on the role of one of the proteolytic actors in the intestinal mucosa, chymotrypsin, and its involvement in the host-microbiota interface.

2021 - 2024

Study of the transmission of the seed microbiota and its impact on the phenotype of young plants

• PhD student: Gontran ARNAULT
• Supervisors: Marie SIMONIN, Matthieu BARRET
• Cofunding: 50% INRAE / 50% Région Pays-de-la-Loire

Despite the central role of seeds in producing food and maintaining plant biodiversity, studies on their microbiota remain in a minority. Because of this, knowledge is still limited regarding the role of this microbiota during the early stages of plant life, particularly during germination and emergence. Seeds have a diversified microbiota but the causal relationships between the composition of the seed microbiota and the phenotype of the young plant have not yet been established. Obtaining a clearer understanding of the dynamics and influence of this microbiota during crop establishment would be particularly valuable because the seed industry is preparing itself for a major revolution regarding the treatment of seeds combined with a reduction in synthetic pesticide use.  In this context, this PhD project proposes to use synthetic ecology approaches in a controlled manner to study the dynamics of a microbiota with a known composition (synthetic community) and its impact on the host phenotype. In particular, the first part of this project will focus on studying transmission of the microbiota from seed to plantlet, in order to determine which fraction actually constitutes the “primary inoculum” of the plant. The second part will evaluate the effects of this microbiota on different plant traits using high-throughput phenotyping by digital imaging, and on characterising the metabolome of the plantlet. Finally, we shall try to identify the strains/consortia and microbial functions involved in modifying the phenotype of the plantlet by means of targeted reconstructions of synthetic communities and comparative genomics.

2020-2023

Impact of interbacterial competition through type VI secretion systems (T6SS) on the dynamics of the seed microbiota

• PhD student: Tiffany GARIN
• Supervisors: Alain SARNIGUET, Matthieu BARRET (IRHS, SPE)
• Cofunding: 50% INRAE / 50% Pays-de-la-Loire

To exploit beneficial seed-microbiota combinations in agriculture, it is necessary to understand the assembly and dynamics of these microbiotas during the early stages of plant development. The habitat offered by seeds is quite small in spatial and resource terms, which induces selection and a major bottleneck for bacterial populations. As a result, the diversity of the seed microbiota tends to be limited, with few dominant taxons when compared with other habitats in the plant. However, considerable diversity is maintained in the microbial assemblies of seeds. The composition and functions of these assemblies can partly be explained by their diversified metabolic capacities. The compositions of microbiotas can also be regulated by interbacterial interactions by means of specific antimicrobial weapons. Some dominant bacterial phyla in seeds are endowed with such weapons, such as type VI secretion systems (orT6SS) that target other micro-organisms with antimicrobial effectors. At present, the contributions of such secretion systems to the assembly of the seed microbiota, and implicitly to seed performance, are not known. This project aims to explore the role of bacterial T6SS in the dynamics of microbiota assembly in brassica seeds and their direct or indirect impact on the transmission of pathogenic agents by seeds.

2021 - 2024

Ecological engineering and maintenance of methane oxidation in photogranules under selection pressure

• PhD student: Sandra GALEA OUTON
• Supervisors: Kim MILFERSTEDT, Jérôme HAMELIN (LBE, MICA)
• Cofunding: 50% INRAE / 50% région Occitanie

We suggest exploring ecosystem functioning of the microbiome in methanotrophic photogranules. Methane removal in photogranules is a potentially fragile ecosystem function as it competes with other heterotrophic processes for oxygen. Finding ways to ecologically engineer a stable methanotrophic community is a prerequisite for a biotechnological application, in which the potent greenhouse gas methane needs to be removed from a waste stream. The PhD student will acquire measurements of photogranule activity as a function of photogranule phenotype, light exposure and competitive pressure resulting from coalescence with allochthonous microbial communities. The data will enable the PhD student to suggest levers that enable the assembly and maintenance of a photogranulated, methanotrophic industrial microbiome removing the greenhouse gas methane from methane-rich effluents. A novel mathematical model bridging the scale of individual photogranules and the bioreactor will be calibrated using the data. An international network of existing collaborations frames this thesis, which will provide opportunities for the PhD candidate.