The PhylHom team focuses on the human microbiome and the impact of xenobiotics (dietary and environmental exposures, drugs, etc) on these complex ecosystems, combining skills in microbial ecology, anaerobic microbiology, and meta-omics. The impact of exposures on the microbiome is determined in a range of health-associated and pathological conditions (neurodevelopment, prematurity, therapy response, inflammatory diseases, cancer, etc.) within translational research projects involving clinicians and epidemiologists.
We have developed an in-vitro pipeline to dynamically assess the impact of biotic and abiotic factors on the host-derived microbiomes. Additionally, we construct synthetic microbial communities from these samples under anaerobic conditions.
Leveraging our expertise in microbial ecology across different ecosystems, we assemble relevant microbial microcosms to elucidate the effects of xenobiotics on microbiota, and consequently on human health. Furthermore, we propose modulation strategies such as nutritional interventions to prevent and/or mitigate detrimental outcomes.
Human microbiomes have a pivotal role in maintaining health and influencing the onset of diseases. Within our team, we are particularly intrigued by microbiome dynamics within the gastrointestinal ecosystem and distal sites like the cervicovaginal cavity. For instance, we actively engage in clinical investigations aimed at pinpointing microbial biomarkers associated with preterm birth associated outcomes, Clostridium sp. infections in neonatal intensive care units, as well as cohorts affected by cancer or chronic diseases. Additionally, we delve into the mechanistic contributions of complex microbial communities, focusing on their involvement in health through examinations of microbe-microbe and microbe-host cell interactions.
Modulating the gut microbiome is of high interest, either to prevent or treat dysbiosis-associated diseases or symptoms. The amplitude of desired modulations depends on the targeted dysbiosis and populations. In the team, we mainly focus on nutritional interventions (for instance, with the purpose of prevention of endocrine disruptors’ deleterious effects or Crohn’s disease patients) and/or fecal microbiota transplantation (as therapeutic support in cancer patients). Our objectives are to disentangle how the beneficial effects of these strategies are mediated by their direct or indirect impact on the gut microbiome.
Microbes are well-known xenobiotic degraders, accumulators, and modifiers. While this is mainly explored in environmental ecosystems such as soil or wastewater, the detoxifying capabilities of human microbiomes are largely overlooked, although constantly exposed to these molecules. To assess both the impact of acute and chronic exposure to xenobiotics (endocrine disruptors, toxins including food toxins, drugs, and emerging contaminants) on the microbiome and the metabolism of these xenobiotics by commensal bacteria, we rely on synthetic microbial communities specific to vulnerable populations (infants, populations with low dietary diversity, populations exposed to PE, patients with inflammatory diseases…) or body sites (intestine, mucosa, vagina etc) to determine the fate of xenobiotics, their impact on these SynCom, and the interactions between these modified microbiomes and the host.
All the team publications are available in the PHYLHOM-MICALIS HAL collection.
Principal past funding sources: ANR (2019, 2018, 2015, 2014, 2013), ANR-DFG (2013), PHRC (2014, 2014), INCa (2016, 2012), IA-RHU (2017), INRAE-Metaprogram (2012).
