A versatile genetic toolbox for Prevotella copri enables studying polysaccharide utilization systems

Abstract

Prevotella copri is a prevalent inhabitant of the human gut and has been associated with plant-rich diet consumption and diverse health states. The underlying genetic basis of these associations remains enigmatic due to the lack of genetic tools. Here, we developed a novel versatile genetic toolbox for rapid and efficient genetic insertion and allelic exchange applicable to P. copri strains from multiple clades. Enabled by the genetic platform, we systematically investigated the specificity of polysaccharide utilization loci (PULs) and identified four highly conserved PULs for utilizing arabinan, pectic galactan, arabinoxylan, and inulin, respectively. Further genetic and functional analysis of arabinan utilization systems illustrate that P. copri has evolved two distinct types of arabinan-processing PULs (PUL Ara ) and that the type-II PUL Ara is significantly enriched in individuals consuming a vegan diet compared to other diets. In summary, this genetic toolbox will enable functional genetic studies for P. copri in future.

Genomic repertoires linked with pathogenic potency of arthritogenic Prevotella copri isolated from the gut of patients with rheumatoid arthritis

“…Phylogenetic analysis was performed based on 284 conserved genes using genome sequences obtained from 15 strains in a previous study, 26 our 13 strains and the reference strain JCM 13464. Consistent with previous studies, 24 26 28 the 13 P. copri strains were genetically categorised into three distinct clades (figure 1A). The majority of the strains (11 out of 13 strains) belonged to clade A.…”

“…[14][15][16][17] However, P. copri is also predominant among the intestinal microbiota of healthy individuals with a diet rich in plant-derived fibre. [20][21][22][23][24][25] Based on the findings of this study, we propose that colonisation of pathogenic P. copri, rather than Prevotella-predominant dysbiosis, in the intestines is one of the causes of RA pathogenesis.…”

“…However, we encountered difficulty in introducing gene modifications into P. copri. Recently, a novel gene tool to introduce gene insertions and deletions into P. copri has been developed, 24 which may aid identification of the pathogenic factor responsible for arthritis development in a future study.…”

“…enzymes in the intestine. [20][21][22][23][24][25] Thus, it is controversial as to whether P. copri is harmful or beneficial to the host.…”

Understanding the Role of Prevotella Genus in the Digestion of Lignocellulose and Other Substrates in Vietnamese Native Goats’ Rumen by Metagenomic Deep Sequencing

“…Some PULs related in arabinan-, xylan-, and galactan-processing were situated in contig 148, 616. The PULs for arabinan-processing were found in Prevotella copri in the human gut [48] but PULs for other polysaccharides degradation, including galactan-, xylan-, and arabinan-processing in Prevotella, were the first observation in this study.…”