MMI-TB Program

FRAMEWORK

• Duration: 2015 – 2021.

• Status: Completed.

• Role: Principal Investigator.

• Funding: Young Investigator JC/JC award, ANR (ANR-15-CE15-0012).

• Principal Investigator: Dr. Geanncarlo Lugo-Villarino, DR2/CNRS.

• Weblink: https://anr.fr/Projet-ANR-15-CE15-0012

• Personnel participating in this project:

  • Dr. Geanncarlo Lugo-Villarino, DR2/CNRS.

  • Dr. Olivier Neyrolles, DRCE/CNRS.

  • Lucie Bernard-Raichon, PhD candidate (2015-2020):

    • 4th-year financed by the FRM scholarship (2018-2019).

  • Hugo Garnier, Master 1/Master 2R candidate (2019-2020).

  • Margaux Cescato, Master 1 candidate (2016-2017).

  • Pauline Guilloton, Master 2R candidate (2014-2015).

  • Ghebrendrias N, Undergraduate student (2015-2016):

    • iREU program/National Science Foundation (NSF) in the USA.

  • Andre Colom, Engineer.

• Collaboration: IPBS/CNRS, Toulouse

  • Partner Team: Dr. Etienne Meunier and Dr. Céline Cougoule

  • Key Personnel: 

    • Dr. Céline Cougoule, CRCN/CNRS

    • Dr. Stephen Leon-Icaza, PhD graduate and post-doctoral fellow

• Collaboration: INRA

  • Country: France.

  • Partner Unit: MICALIS Institute, Jouy-en-Josas.

  • Partner Team: Drs. Philippe Langella, Muriel Thomas, and Aude Remot.

  • Collaboration context: Collaboration established between IPBS/CNRS and MICALIS institute/INRA within the framework of a "JCJC" ANR grant to study how microbiota influences the immune response to tuberculosis.

• Socio-economic valorization: 

  • Bernard-Raichon Lψ, Thomas M, Remot A, Langella P, Neyrolles O, Lugo-Villarino G. “Treatment of respiratory diseases using the bacteria Lactobacillus animalis”. 2020. N° FR1903364 (France)/PCT N°EP2020/058832 (International); ψsupervised student.

A. Role of Pulmonary Microbiota in Modulating Lung Immunity during Tuberculosis 

• Student: Lucie Bernard-Raichon (PhD defended in 2020)

• Supervisor: Geanncarlo Lugo-Villarino

SUMMARY: The lungs harbor resident microbial communities that are increasingly recognized as important regulators of respiratory immunity. Yet, whether specific members of the pulmonary microbiota can directly shape lung immune responses and influence host–pathogen interactions during TB remains poorly understood. In this study, we investigated the immunomodulatory properties of a commensal bacterium, Lactobacillus murinus CNCM I-5314, originally isolated from the lungs of neonatal mice. 

We demonstrated that intranasal administration of this bacterial strain selectively reshapes the lung CD4⁺ T cell compartment. In naïve mice, pulmonary delivery of CNCM I-5314 significantly increased the abundance of Th17 cells and of a specialized subset of regulatory T cells co-expressing Foxp3 and RORγt (RORγt⁺ Tregs), whereas conventional Tregs remained largely unchanged. This effect was primarily local, as intragastric administration had only a limited impact on lung T cells. Phenotypic analyses further revealed that these Th17 and RORγt⁺ Tregs exhibited features consistent with immunomodulatory functions, including expression of regulatory receptors such as CTLA-4 and PD-1 and cytokine profiles compatible with tissue regulation rather than overt inflammation. 

Importantly, this immunomodulatory activity persisted during experimental Mtb infection. Mice treated with CNCM I-5314 displayed increased numbers of lung Th17 cells and RORγt⁺ Tregs without affecting the protective Th1 response required for bacterial control. Although bacterial loads in the lung and spleen remained unchanged, histological and immunological analyses revealed a significant reduction in pulmonary inflammation, characterized by decreased leukocyte infiltration and reduced abundance of inflammatory monocytes. These changes were accompanied by a shift in macrophage populations toward a tissue-repair phenotype.

SIGNIFICANCE: This work provides experimental evidence that specific members of the lung microbiota can actively regulate local immune homeostasis and modulate inflammatory responses during chronic lung infection. By identifying airway commensal bacteria as key regulators of host–pathogen interactions, this study opens new perspectives for microbiota-based or host-directed strategies to limit immunopathology in tuberculosis and other respiratory diseases. These results were published in The Journal of Immunology in 2021, with Lucie Bernard-Raichon as first author, Céline Cougoule, Olivier Neyrolles, and me as last authors (Bernard-Raichon et al., J Immunol, 2021).

B. Development of a Microbiota-Based Therapeutic Strategy to Limit Lung Inflammation in Tuberculosis

• Inventors: Bernard-Raichon Lψ, Thomas M, Remot A, Langella P, Neyrolles O, Lugo-Villarino G.

• Patent: Use of pulmonary Lactobacillus strains for the prevention or treatment of inflammatory respiratory diseases (PCT WO2020201145A1).

SUMMARY: Building on our discovery that the pulmonary commensal bacterium Lactobacillus murinus CNCM I-5314 modulates lung immune responses and reduces TB-associated inflammation, we pursued the translational potential of this finding by developing a patent-protected microbiota-based therapeutic approach. The bacterial strain characterized in our study was isolated from neonatal mouse lungs and deposited at the French National Collection of Microorganism Cultures (CNCM) under the identifier CNCM I-5314. 

The patent application describes the use of this lung Lactobacillus strain, or related immunomodulatory bacterial preparations, to prevent or treat inflammatory respiratory diseases. Our experimental findings demonstrated that intranasal administration of CNCM I-5314 induces a balanced immune response in the lung characterized by the expansion of Th17 cells and RORγt⁺regulatory T cells, while simultaneously reducing the recruitment of inflammatory monocytes and limiting tissue-damaging inflammation during Mtb infection. Importantly, this immunomodulatory effect occurs without increasing bacterial burden, suggesting that the bacterium promotes immune regulation rather than compromising host defense. 

Based on these observations, the patented strategy proposes using pulmonary commensal bacteria as next-generation probiotics to restore immune homeostasis in the respiratory tract. Such approaches may be particularly relevant for chronic inflammatory lung diseases, including TB, asthma, and chronic obstructive pulmonary disease, in which dysbiosis of the lung microbiota and dysregulated immune responses contribute to pathology.

SIGNIFICANCE: This work illustrates how fundamental discoveries on the immunological functions of the pulmonary microbiota can be translated into innovative therapeutic strategies. By identifying a lung-resident Lactobacillus strain that limits infection-associated inflammation without impairing antimicrobial immunity, this patent establishes a framework for microbiota-based interventions to control immunopathology in respiratory diseases.