Phylogenetics And Comparative Genomics Of Prevotella In Gut

Prevotella is not only one of the three enterotypes,but also the core bacteria genus of human gut microbiota.Several studies have shown that Prevotella or P.copri is positively associated with insulin resistance,rheumatoid arthritis,and hypertension,while negatively correlated with Parkinson's disease and autism.For such important intestinal microorganisms,however,there are many deficiencies or even blanks in their taxonomy and basic biology research.On the one hand,there is a lack of systematic understanding of the phylogenetic relationship and taxonomy of this genus or even this family.On the other hand,the features of genome content,metabolic properties and differences of population distribution also urgently need to answer.Based on the above factors,through combining bioinformatics with anaerobic pure culture experiment,we use public metagenomic data of gut microbiome and laboratory investigations to study the phylogeny,host distribution of Prevotella genus and comparative genomics analysis of P.copri species in a global scale.We have also tried to design the primers for different taxonomic precision of Prevotella genus based on the results of phylogeny and comparative genomics analysis.The results showed that;1)Comprehensively utilizing the 16S rRNAgene and gyrB gene from the IGC database for phylogenetic analysis,we firstly reveal the existence of P.copri phylogenetic clade which is specifically symbiotic in the intestinal tract of mammals and evolves relatively independently in the Prevotella genus.2)Based on the deep-mining the data from IGC database as well as the population survey experiments conducted in Fuzhou and Xiamen,we discover that compared to European and American populations,P.copri phylogenetic clade performs a higher frequency and abundance in the Chinese gut.We speculate that this phenomenon may be associated with Chinese dietetical characteristic.3)We totally bin 103 high quality draft genomes of P.copri by collecting more than 1700 metagenomic data of human gut microbiome from the world and combining with strains isolated in this study.Based on the phylogenomic-based phylogenetic analysis,we find that P.copri has extremely high diversity at the genome level,and there is a clear difference in biogeographic distribution within the species.The strains of Chinese origin mainly form two groups,and there is metabolic specificity within the group.4)Five strains of P.copri phylogenetic clade within the group are isolated from human feces by anaerobic pure culture,including 2 strains of potential new species of the P.copri phylogenetic clade and 2 P.copri strains from Chinese origin as well as belonging to the Group 2.This compensates for the lack that there is only one public reference genome of P.copri all over the world currently.5)We design different primers for specific biomarker genes of Prevotella genus,P.copri phylogenetic clade and P.copri species(theoretically to subspecies or even strain levels).This will provide a reliable technical foundation for future accurately qualitative and quantitative studies ofP.copri phylogenetic clade and P.copri species.