1. An update on current methods for studying microbiome-host interactions in health and diseases
Abstract
The intestinal microbiota is considered as a true organ, playing major roles for its host. Dysbiosis has been shown in a number of diseases including inflammatory bowel diseases, metabolic disorders but also neurological disorders. However, little is known about the underlying mechanisms. In the present review, we attempted to summarize the different methods developed and used to study microbiota-host interactions and their limitations. Among the factors limiting our current understanding of the mechanisms of interaction between the gut microbiota and host cells, the difficulty of culturing most commensal bacteria and the complexity of the culture medium are of particular importance. The development of metagenomic approaches has been a decisive step towards understanding the functions of the intestinal microbiota. We have therefore developed a high-throughput functional metagenomic approach to overcome these limitations and identify bacterial genes and compounds regulating key signalling pathways or effector genes in mammalian immune, intestinal or liver cells. Genomic and metagenomic libraries were constructed by cloning large DNA fragments into a fosmid vector and using E. coli as the host. A highthroughput screening platform was established, enabling the identification of clones modulating pathways and genes in mammalian cells. Although the host is a gram-negative bacterium, it was possible to identify genes derived from the 3 main phyla present in the gut, namely Bacillota, Bacteroidota and Actinomycetota. This functional metagenomic strategy allowed to characterize new genes from commensal bacteria and effector molecules that have an impact on the host's cellular functions, with a potential influence on mammalian health.
Related
- In vivo CAR-T for the treatment of autoimmune diseases: Current progress and future directions
- Designing fiber–gut microbiome interactions with active learning
- Probiotic-hydrogel systems for microbiome-associated diseases: design principles, preclinical evidence, and translational challenges.
- Gut Microbiome Dysbiosis in Metabolic Syndrome: Current Evidence and Emerging Perspectives
- Protease-serpin-microbiome interactions in inflammatory bowel disease: toward integrated biomarkers of gut health
BibTeX
@article{naour2026update,
title = {{1. An update on current methods for studying microbiome-host interactions in health and diseases}},
author = {Maxime Naour and Chaima Ezzine and Catherine Michel and Elliot Mathieu and Véronique Lejard and Gwenola Le Dréan and Jean-Marc Lelièvre and Nicolas Lapaque and Joël Doré and Hervé M Blottière},
journal = {Animal. Science proceedings},
year = {2026},
month = oct,
doi = {10.1016/j.anscip.2025.07.002},
url = {https://hal.inrae.fr/hal-05783203v1},
note = {CC BY-NC-ND 4.0},
}
RIS
TY - JOUR
TI - 1. An update on current methods for studying microbiome-host interactions in health and diseases
AU - Maxime Naour
AU - Chaima Ezzine
AU - Catherine Michel
AU - Elliot Mathieu
AU - Véronique Lejard
AU - Gwenola Le Dréan
AU - Jean-Marc Lelièvre
AU - Nicolas Lapaque
AU - Joël Doré
AU - Hervé M Blottière
PY - 2026
DA - 2026/10/07
JO - Animal. Science proceedings
DO - 10.1016/j.anscip.2025.07.002
UR - https://hal.inrae.fr/hal-05783203v1
AB - The intestinal microbiota is considered as a true organ, playing major roles for its host. Dysbiosis has been shown in a number of diseases including inflammatory bowel diseases, metabolic disorders but also neurological disorders. However, little is known about the underlying mechanisms. In the present review, we attempted to summarize the different methods developed and used to study microbiota-host interactions and their limitations. Among the factors limiting our current understanding of the mechanisms of interaction between the gut microbiota and host cells, the difficulty of culturing most commensal bacteria and the complexity of the culture medium are of particular importance. The development of metagenomic approaches has been a decisive step towards understanding the functions of the intestinal microbiota. We have therefore developed a high-throughput functional metagenomic approach to overcome these limitations and identify bacterial genes and compounds regulating key signalling pathways or effector genes in mammalian immune, intestinal or liver cells. Genomic and metagenomic libraries were constructed by cloning large DNA fragments into a fosmid vector and using E. coli as the host. A highthroughput screening platform was established, enabling the identification of clones modulating pathways and genes in mammalian cells. Although the host is a gram-negative bacterium, it was possible to identify genes derived from the 3 main phyla present in the gut, namely Bacillota, Bacteroidota and Actinomycetota. This functional metagenomic strategy allowed to characterize new genes from commensal bacteria and effector molecules that have an impact on the host's cellular functions, with a potential influence on mammalian health.
SN - 2772-283X
ER -