Functional Characterization of Novel Faecalibacterium prausnitzii Strains Isolated from Healthy Volunteers: A Step Forward in the Use of F. prausnitzii as a Next-Generation Probiotic.

Philippe Langella,Jean M. Chatel,Sylvie Hudault,Vasco Azevedo,Florian Chain,Luis G. Bermúdez-Humarán,Olivier Berteau,Leandro Benevides,Muriel Thomas,Véronique Robert,Chantal Bridonneau,Rebeca Martín,Harry Sokol,Sylvie Miquel

doi:10.3389/fmicb.2017.01226

Abstract

Faecalibacterium prausnitzii is a major member of the Firmicutes phylum and one of the most abundant bacteria in the healthy human microbiota. F. prausnitzii depletion has been reported in several intestinal disorders, and more consistently in Crohn's disease (CD) patients. Despite its importance in human health, only few microbiological studies have been performed to isolate novel F. prausnitzii strains in order to better understand the biodiversity and physiological diversity of this beneficial commensal species. In this study, we described a protocol to isolate novel F. prausnitzii strains from feces of healthy volunteers as well as a deep molecular and metabolic characterization of these isolated strains. These F. prausnitzii strains were classified in two phylogroups and three clusters according to 16S rRNA sequences and results support that they would belong to two different genomospecies or genomovars as no genome sequencing has been performed in this work. Differences in enzymes production, antibiotic resistance and immunomodulatory properties were found to be strain-dependent. So far, all F. prausnitzii isolates share some characteristic such as (i) the lack of epithelial cells adhesion, plasmids, anti-microbial, and hemolytic activity and (ii) the presence of DNAse activity. Furthermore, Short Chain Fatty Acids (SCFA) production was assessed for the novel isolates as these products influence intestinal homeostasis. Indeed, the butyrate production has been correlated to the capacity to induce IL-10, an anti-inflammatory cytokine, in peripheral blood mononuclear cells (PBMC) but not to the ability to block IL-8 secretion in TNF-α-stimulated HT-29 cells, reinforcing the hypothesis of a complex anti-inflammatory pathway driven by F. prausnitzii. Altogether, our results suggest that some F. prausnitzii strains could represent good candidates as next-generation probiotic.

Highlights

Despite a large number of bacteria, archaea, viruses, and unicellular eukaryotes inhabit the human body, only a few bacterial genera (Bacteroides, Clostridium, Bifidobacterium, and Faecalibacterium) predominate in the human gut microbiome (Schmidt, 2013)
A negative screening was performed through the exposition of bacterial isolates to oxygen and in parallel, these same strains were cultivated in an anaerobic chamber, which maintains a consistent anaerobic environment to ensure proper conditions for optimal Extremely Oxygen Sensitive (EOS) growth
We identified between 28.1 and 67.7% of EOS strains in the microbiota of healthy volunteers (Table 1)

Summary

Introduction

Despite a large number of bacteria, archaea, viruses, and unicellular eukaryotes inhabit the human body, only a few bacterial genera (Bacteroides, Clostridium, Bifidobacterium, and Faecalibacterium) predominate in the human gut microbiome (Schmidt, 2013). The levels of F. prausnitzii have been found to be decreased in patients suffering from intestinal and metabolic disorders such as inflammatory bowel diseases (IBD), irritable bowel syndrome (IBS), colorectal cancer (CRC), obesity, and celiac disease among others (Balamurugan et al, 2008; Sokol et al, 2008; Neish, 2009; De Palma et al, 2010; Furet et al, 2010; Rajilic-Stojanovic et al, 2011) as well as in frail elderly (van Tongeren et al, 2005) This species may be a biomarker of choice to assist in Ulcerative colitis (UC) and Crohn’s disease (CD) discrimination (Lopez-Siles et al, 2017). Most of the data referring F. prausnitzii are based on metagenomic studies (Miquel et al, 2013), with only few studies with isolated strains and functional approach (Duncan et al, 2002; Ramirez-Farias et al, 2009; Lopez-Siles et al, 2012; Foditsch et al, 2014) This gap between metagenomic and microbiological data is striking for microbiota-derived EOS bacteria. It is essential to increase the knowledge of several commensal bacterial strains in order to better understand the beneficial effect of this species

Objectives

Methods

Results

Conclusion