Publications

Investigation of the link between mother’s obesity & regulation of the child’s appetite through microbiota. This in vivo study suggests that neonatal gut microbiotal transfer can program eating behavior.

Individuals with severe IBS are characterized by a higher intake of poorer-quality food items during their main meals. Our analysis suggested that covariations between gut microbiota at subspecies level and diet could be explained with IBS symptom severity, exhaled gas, glycan metabolism, and meat/plant ratio. We provided evidence that IBS severity is associated with altered gut microbiota hydrogen function in correlation with microbiota enzymes involved in animal carbohydrate metabolism.

The Human Gut Microbiome Atlas (HGMA) provides i) quantitative information of global shotgun metagenomics of human gut microbiome ii) function/phenotype information of the human gut-associated metagenomic species pan-genomes (MSP) and iii) provide global map of human gut microbiome. Global shotgun metagenomics of normal human gut microbiome from 18 countries are presented with i) species abundance, ii) gene richness and iii) enterotypes. In addition, comprehensive analysis enabled the identification of species enriched/depleted in 20 different diseases with functions/phenotype of respective species, detailing the dysbiosis in gut microbiome composition.

Mediterranean diet-induced Arrangement of the Gut Microbiome for Improvement of Cardiometabolic Health
In this study, authors show the Mediterranean diet (MD) effect on the gut microbiome composition and its effect on the endocannabinoid system involved in the development of obesity and its comorbidities
Endocannabinoid tone and microbiome functionality at baseline drives an individualised response to an MD in ameliorating insulin sensitivity and inflammation
MD impacts gut microbiome composition with an increase of Akkermansia muciniphila

Microbiome functional analysis reveals changes in carbohydrate-active enzymes in PD
Higher number of bacterial mucin and host degradation enzymes link to PD
Metabolic modeling reveals the contribution of bacterial-specific metabolism in PD
L'analyse systématique du microbiome intestinal révèle le rôle du métabolisme bactérien des folates et de l'homocystéine dans la maladie de ParkinsonGut-community modeling reveals the role of bacterial folate and homocysteine in PD

The number of indications for fecal microbiota transplantation is expected to rise, thus increasing the needs for production of readily available frozen or freeze-dried transplants. Using shotgun metagenomics, we investigated the capacity of two novel human fecal microbiota transplants prepared in maltodextrin-trehalose solutions (abbreviated MD and TR for maltodextrin:trehalose, 3:1, w/w, and trehalose:maltodextrin 3:1, w/w, respectively), to colonize a germ-free born mouse model. Gavage with frozen-thawed MD or TR suspensions gave the taxonomic profiles of mouse feces that best resembled those obtained with the fresh inoculum (Spearman correlations based on relative abundances of metagenomic species around 0.80 and 0.75 for MD and TR respectively), while engraftment capacity of defrosted NaCl transplants most diverged (Spearman correlations around 0.63). Engraftment of members of the family Lachnospiraceae and Ruminoccocaceae was the most challenging in all groups of mice, being improved with MD and TR transplants compared to NaCl, but still lower than with the fresh preparation. Improvement of engraftment of this important group in maintaining health represents a challenge that could benefit from further research on fecal microbiota transplant manufacturing.

Analysis of metaproteomics data is of high interest since it reveals the functions actually operating in the microbiome. However, handling large sample size remains challenging.
This study describes how to improve the data analysis strategy for interpreting human gut metaproteomics data, with an elaborate iterative database search

Finlay et al. PNAS 2021
In this publication, authors explore many facets of COVID-19−induced societal changes and their possible effects on the microbiome, and discuss current and future challenges regarding the interplay between this pandemic and the microbiome. Recent recognition of the microbiome’s influence on human health makes it critical to consider both how the microbiome, shaped by biosocial processes, affects susceptibility to the coronavirus and, conversely, how COVID-19 disease and prevention measures may affect the microbiome. This knowledge may prove key in prevention and treatment, and long-term biological and social outcomes of this pandemic.

D. Burz et al. Microorganisms 2021
In this study, authors transplanted the microbiota from a patient with fatty liver (NAFL) and from a healthy individual to two groups of mice. We first showed that the microbiota composition in recipient mice resembled the microbiota composition of their respective human donor. Following administration of a high-fructose, high-fat diet, mice that received the human NAFL microbiota (NAFLR) gained more weight and had a higher liver triglycerides level and higher plasma LDL cholesterol than mice that received the human healthy microbiota (HR). Metabolomic analyses revealed that it was associated with lower and higher plasma levels of glycine and 3-Indolepropionic acid in NAFLR mice, respectively. Moreover, several bacterial genera and OTUs were identified as differently represented in the NAFLR and HR microbiota and therefore potentially responsible for the different phenotypes observed. Altogether, our results confirm that the gut bacteria play a role in obesity and steatosis development and that targeting the gut microbiota may be a preventive or therapeutic strategy in NAFLD management.