Comprehensive analysis of 84 Faecalibacterium prausnitzii strains uncovers their genetic diversity, functional characteristics, and potential risks

Abstract

Faecalibacterium prausnitzii is a beneficial human gut microbe and a candidate for next-generation probiotics. With probiotics now being used in clinical treatments, concerns about their safety and side effects need to be considered. Therefore, it is essential to obtain a comprehensive understanding of the genetic diversity, functional characteristics, and potential risks of different F. prausnitzii strains. In this study, we collected the genetic information of 84 F . prausnitzii strains to conduct a pan-genome analysis with multiple perspectives. Based on single-copy genes and the sequences of 16S rRNA and the compositions of the pan-genome, different phylogenetic analyses of F. prausnitzii strains were performed, which showed the genetic diversity among them. Among the proteins of the pan-genome, we found that the accessory clusters made a greater contribution to the primary genetic functions of F. prausnitzii strains than the core and specific clusters. The functional annotations of F. prausnitzii showed that only a very small number of proteins were related to human diseases and there were no secondary metabolic gene clusters encoding harmful products. At the same time, complete fatty acid metabolism was detected in F. prausnitzii. In addition, we detected harmful elements, including antibiotic resistance genes, virulence factors, and pathogenic genes, and proposed the probiotic potential risk index (PPRI) and probiotic potential risk score (PPRS) to classify these 84 strains into low-, medium-, and high-risk groups. Finally, 15 strains were identified as low-risk strains and prioritized for clinical application. Undoubtedly, our results provide a comprehensive understanding and insight into F. prausnitzii, and PPRI and PPRS can be applied to evaluate the potential risks of probiotics in general and to guide the application of probiotics in clinical application.

Lectin-Seq: A method to profile lectin-microbe interactions in native communities

“…The plant lectins were effective competitors, suggesting that the human lectin binds the same F. prausnitzii glycans. These results are further supported by a recent genome analysis of 84 F. prausnitzii strains, which found that all genomes analyzed contain genes from the GT94 glycosyltransferase family ( 41 ). GT94 is composed of a mannosyltransferase that catalyzes the addition of alpha-linked mannose residues to xanthan chains in exopolysaccharide ( 42 ).…”

Anaerostipes hadrus , a butyrate-producing bacterium capable of metabolizing 5-fluorouracil

“…We found that the proportion of core gene families in A. hadrus pan-genome (2.7%) is slightly lower than in other species (3%–84%) ( 64 ). Compared with other butyrate-producing bacteria, including F. prausnitzii [4.5% of core gene families in the pan-genome constructed by 84 strains ( 65 )], Clostridium perfringens [3.8% of core gene families in the pan-genome constructed by 173 strains ( 66 )], and Clostridium butyricum [9.9% of core gene families in the pan-genome constructed by 32 strains ( 67 )], A. hadrus had a smaller core genome, suggesting the functional diversity and complexity. The phylogenetic and functional annotation analysis results showed no noticeable geographical distribution differences among different A. hadrus clades ( Fig.…”

Targeted remodeling of the human gut microbiome using Juemingzi (Senna seed extracts)

“…While multiple other members of the Bacillota decreased in both relative and absolute abundance, F. prausnitzii increased in abundance relative to controls ( Figure 6 , Supplementary Figure 2 ). F. prausnitzii is noted for its ability to produce butyrate ( Miquel et al., 2014 ), fructose ( Fagundes et al., 2021 ) and to generate proteins with host anti-inflammatory effects ( Miquel et al., 2015 ; Quévrain et al., 2016 ; Lenoir et al., 2020 ) and members of this taxon have generally been associated with good gastrointestinal health ( Bai et al., 2023 ). Reductions in F. prausnitzii have been particularly associated with conditions such as Crohn’s Disease/Ulcerative Colitis and colorectal cancer ( Bai et al., 2023 ).…”

“…F. prausnitzii is noted for its ability to produce butyrate ( Miquel et al., 2014 ), fructose ( Fagundes et al., 2021 ) and to generate proteins with host anti-inflammatory effects ( Miquel et al., 2015 ; Quévrain et al., 2016 ; Lenoir et al., 2020 ) and members of this taxon have generally been associated with good gastrointestinal health ( Bai et al., 2023 ). Reductions in F. prausnitzii have been particularly associated with conditions such as Crohn’s Disease/Ulcerative Colitis and colorectal cancer ( Bai et al., 2023 ). The abundance of F. prausnitzii and the ratio of F. prausnitzii (Fc) to E. coli (Ec) have been suggested as a biomarkers to discern healthy GIT and between GIT disease conditions respectively ( Lopez-Siles et al., 2017 ) In our study, the Fc/Ec ratio decreased from inoculum to incubated samples, but did not differ markedly between controls and treated samples.…”