Distinct polysaccharide growth profiles of human intestinalPrevotella copriisolates

Abstract

The gut-dwelling Prevotella copri, the most prevalent Prevotella species in human gut, have been associated with diet as well as disease, but our understanding of their diversity and functional roles remains rudimentary, as studies have been limited to 16S and metagenomic surveys and experiments using a single type strain. Here, we describe the genomic diversity of 83 P. copri isolates from 11 donors. We demonstrate that genomically distinct isolates, which can be categorized into different P. copri complex clades, utilize defined sets of plant polysaccharides that can be predicted in part from their genomes and from metagenomic data.This study thus reveals both genomic and functional differences in polysaccharide utilization between several novel human intestinal P. copri strains.

Effect of Lactylate and Bacillus subtilis on Growth Performance, Peripheral Blood Cell Profile, and Gut Microbiota of Nursery Pigs

“…From weaning to NP1, there were significant differences in microbiota composition due to various available fiber sources and other undigested compounds in the distal gut. For instance, Prevotella copri was observed to develop rapidly during this period due to the increased plant fiber in the diet [ 38 ]. Their relative abundance increased during NP2 and then slightly decreased in NP3.…”

The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations

“…Stool was collected into anaerobic transport media (Anaerobe Systems), then streaked on BRU and LKV plates (Anaerobe Systems). After 24-48h, individual colonies were picked and screened with Prevotella -specific PCR primers, and the 16S rRNA V3-V4 sequence was confirmed by Sanger sequencing (Fehlner-Peach et al., 2019). Prevotella -positive isolates were grown on BRU plates, and mature colonies were collected for genomic DNA isolation with the PowerSoil DNA isolation kit (Qiagen).…”

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

“…was found in populations consuming a plant-rich diet, e.g., vegetarians in Western populations (De Filippo et al, 2010;Wu et al, 2011;Ruengsomwong et al, 2016;Fragiadakis et al, 2019), suggesting that they encode efficient machineries for degradation of plant-derived polysaccharides. Yet, due to the lack of genetic tools, the characterization of carbohydrate utilization has been limited to bioinformatic and phenotypic studies (De Filippis et al, 2019;Fehlner-Peach et al, 2019). Specifically, two recent studies described extensive variability among clades and also strains within clades in the ability to directly utilize diverse complex plant carbohydrates (Fehlner-Peach et al, 2019;Tett et al, 2019).…”

“…Yet, due to the lack of genetic tools, the characterization of carbohydrate utilization has been limited to bioinformatic and phenotypic studies (De Filippis et al, 2019;Fehlner-Peach et al, 2019). Specifically, two recent studies described extensive variability among clades and also strains within clades in the ability to directly utilize diverse complex plant carbohydrates (Fehlner-Peach et al, 2019;Tett et al, 2019). While combinations of comparative genomics and phenotypic assays can be used to predict the ability to utilize specific polysaccharides, such approaches rely on wellcharacterized genetic elements as a reference, which makes it difficult to identify genes with unknown functions and thereby hinders the establishment of casual relationship between the genetic content and phenotypes.…”