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To test whether P. copri could influence inflammation, the team administered the bacteria to healthy mice so that the bacteria became part of their gut microbiome. https://doi.org/10.1111/j.1600-051X.2005.00782.x (2005). Funct. 7a). Von Meijenfeldt, F. A. De Filippis, F. et al. Ecol. Nature https://doi.org/10.1038/nature12820 (2014). Nat. 7d). https://doi.org/10.1128/AEM.00402-17 (2017). c Increase in PERMANOVA R2 values using the relative abundance of 15 VFs showed higher abundance in western populations, 118 VFs showed higher abundance in non-western populations, and 25 differentially abundant VFs in western populations. Next level of bin refinement was carried out on the basis of taxonomic annotation of all contigs in each bin using CAT99. Microbiol. Environ. The differentially abundant Prevotella genomes in western IBD patients also showed higher abundance in the western-healthy population in comparison with non-western-healthy populations (Supplementary Fig. BMC Bioinformatics https://doi.org/10.1186/1471-2105-11-367 (2010). The second most frequent pullulanase-containing-PUL has GH43_4 and GH43_5 shown as (ii) with the aforementioned CAZy gene families and is present in 93 genomes (with the same arrangement of CAZy families). Commensal-specific CD4+ cells from patients with Crohns disease have a T-helper 17 inflammatory profile. Outlook on next-generation probiotics from the human gut 18a, b). Until sequencing, all the DNA samples were stored at 80C. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Commun. To investigate whether virulence-related genes are prevalent in gut Prevotella species, we searched our Prevotella gene catalog for homologies to genes in the bacterial virulence factor databases49,50. Gomez, A. et al. Prevotella genomes from the Spanish population contained the most antibiotic resistance genes, followed by US and Italian populations, when both strict and loose criteria were applied with the resistance gene identifier. However, metronidazole is a broad-spectrum antibiotic that is mainly used for anaerobic bacteria, it . Sci. The abundance of each Prevotella genome in human gut samples was calculated by alignment of reads against this Prevotella genome database (Supplementary Note 2, Supplementary Figs. & Pevzner, P. A. MetaSPAdes: a new versatile metagenomic assembler. The results provide fundamental knowledge for . Several studies have also reported the increase in abundance of Prevotella with the supplementation of wheat bran arabinoxylan oligosaccharides (AXOS)80,81,82. Immunol. carried out all metagenomic data and statistical analysis, interpretation of results, and prepared the first draft of the manuscript under the supervision of V.K.S. Of the 133 virulence protein genes identified in the core data set (see Methods section), 118 had a higher average relative abundance in western populations compared to non-western populations, and the remaining 15 showed higher abundance in non-western populations (Supplementary Fig. All possible genes from genomes belonging to the Prevotella genus have been considered for this analysis. Immunol. Preprint at bioRxiv https://doi.org/10.1101/421024 (2018). CheckM96 (1.1.2) was used to quantify the quality of bins produced. Genomes highlighted in a lighter shade of red color are differentially abundant in the IBD cohort, and genomes highlighted in a lighter shade of green color are differentially abundant in the healthy cohort. https://doi.org/10.1093/nar/gki008 (2005). Rev. Relative abundance was calculated after classifying reads at the genus level using Kaiju. The pairwise intergenomic distances of each genome/bin were calculated, and the MASH distance-based clustering resulted in 9 bins assigned to clade C, 7 bins assigned to clade B, and 5 bins assigned to clade A. Alpha-beta diversity and PERMANOVA (with permutations = 999) analyses was carried out using vegan111 and ape112 R-packages. y Microbiol. Since its discovery in 2007, the importance of the human gut bacterium Prevotella copri (P. copri) has been widely recognized with its links to diet and health status and potential as next generation probiotic. https://doi.org/10.1093/jac/dkn079 (2008). Carbohydrate metabolism is a key function of several dominant Prevotella species in the gut, thus we compared the abundance of genes involved in carbohydrate metabolism in the Prevotella genomes from the various populations using CAZy (carbohydrate-active enzymes) database42 (details in Supplementary Note 8). Shannon, P. et al. Gut microbiome structure and metabolic activity in inflammatory bowel disease. David, L. A. et al. Protein Cell https://doi.org/10.1007/s13238-011-1105-3 (2011). oral taxon 820 and Prevotella sp. Nature https://doi.org/10.1038/s41586-019-1058-x (2019). De Vadder, F. et al. (3) Environment CCREPE package in R was used for correlation analysis and cytoscape118 was used for plotting co-occurrence plots using significant correlation values. The unique composition of Indian gut microbiome, gene catalogue, and associated fecal metabolome deciphered using multi-omics approaches. (English ed.) This Editorial aims to clarify the role of specific genus of gut microbiota, such as Prevotella, in influencing the pathogenesis of Rheumatoid Arthritis (RA). Van Winkelhoff, A. J., Herrera, D., Oteo, A. Thus, in this study, a comprehensive analysis of the composition, diversity, and functional role of Prevotella species in the gut microbiome was carried out in Prevotella-rich non-western populations (Madagascar, Tanzania, and Peru)10,12,13,14,33 including the largest gut metagenome of the Indian population that primarily consume plant-based diets, and western populations (US, Spain, Netherlands, and Italy)9,19,34 that primarily consume the animal-based diets. e Alpha-diversity measure (using Shannon index) of Prevotella ARGs in all healthy populations. Dhakan, D. B. et al. Anim. https://doi.org/10.1016/j.eimce.2017.06.005 (2017). Abstract Prevotella copri is a prevalent inhabitant of the human gut and has been associated with plant-rich diet consumption and diverse health states. Protein homology search of genes in PGC against both core and full data set using DIAMOND and best hits having score60 and e-value < 106 were considered for calculating VF gene abundance. Prevotella genus is highlighted in a lighter shade of green color. a Discriminating carbohydrate metabolizing gene families (CAZy families) of Prevotella in the Indian cohort compared to all other populations together (Italy, Netherlands, US, Madagascar, Peru, and Tanzania) identified based on LDA score (using LEfSe). Softw. Prevotella Copri and Microbiota in Rheumatoid Arthritis: Fully - PubMed Fujii, R. et al. NLRP6 inflammasome regulates colonic microbial ecology and risk for colitis. Higher R-squared value obtained using differentially abundant antibiotic resistance genes showed higher abundance in the western population, and these genes also discriminated between western and non-western populations (Fig. Kaoutari, A. El, Armougom, F., Gordon, J. I., Raoult, D. & Henrissat, B. Cell Host Microbe https://doi.org/10.1016/j.chom.2019.10.013 (2019). The majority of the remaining pullulanase-containing-PULs have the same gene families with different arrangements (see Supplementary Notes-part 10 and 11). Int. Of these, P. intermedia, P. marseillensis, and P. lascolaii, are key pathogens that cause anaerobic infections in humans45,46,47, and were significantly abundant in western populations. contracts here. a Principal coordinates analysis considering inter-sample BrayCurtis distance based on the relative abundance of genes from PGC (Prevotella Gene Catalog) in healthy populations. in ulcerative colitis. The core data set includes genes associated with experimentally verified VFs only, whereas the full data set covers all genes related to known and predicted VFs in the database. Interestingly, the oral Prevotella spp. One of the key findings of the study is the identification of PULs containing pullulanase (GH13_14) and other CAZy families including GH77, GH97, GH13, GH43_4, GH43_5, and GH51, which provide evidence for the presence of complex starch and non-starch plant-polysaccharide metabolizing enzymes including some hypothetical genes in same genomic loci in P. copri genomes. 7030 genes having cumulative proportion 0.01 were used for beta-diversity analysis. Classification of populations as western or non-western was made on the basis of traditional lifestyle, diet, and geographic and sociodemographic definitions10,35. 102 Prevotella genomes/bins with indval score >0.60 (p-value < 0.01) were differentially abundant in western and non-western populations and were considered for further analysis. Kleessen, B., Kroesen, A. J., Buhr, H. J. Correspondence to In contrast, the western populations displayed a higher genetic diversity in Prevotella species including P. intermedia, P. oris, P. oralis, P. dentalis (infection related), P. bergensis (infection related), and P. brevis (infection-related), which are also reported to be a part of the oral microbiome in western populations and have been associated with oral inflammatory conditions46,47,56,57,58. (Fig. Principal coordinates analysis revealed a clear separation between western and non-western populations, and the variance explained by PCo-1 increased to 31.6% using relative abundance of these 30 genomes (Supplementary Fig. Med. Prevotella copri is a common human gut microbe that has been both positively and negatively associated with host health. Chen, L. et al. The gut microbiome modulates the protective association between a Mediterranean diet and cardiometabolic disease risk. The Indian samples also showed the highest inter-sample variation among the non-western populations, whereas little inter-sample variation was observed in western populations compared to non-western populations. https://doi.org/10.17796/jcpd.32.3.vp657177815618l1 (2008). Prevotella copri is a gram-negative bacteria. Mittal, P., Saxena, R., Gupta, A., Mahajan, S. & Sharma, V. K. The gene catalog and comparative analysis of gut microbiome of big cats provide new insights on Panthera species. The identification of pullulanase-containing PULs and clusters of complex plant-polysaccharide metabolism genes in P. copri clades also suggests the role of this species in complex polysaccharide metabolism in the gut microbiome of non-western populations. Rep. 7, 113 (2017). Feed Sci. Vitaglione, P. et al. All genomes/bins were assigned till Prevotellaceae family with support value per rank >0.70 and 1610 genomes were assigned till Prevotella genus with support value per rank >0.70 (Supplementary Data 4). Mtt, J. et al. Ondov, B. D. et al. Samples from Italy and Spain showed a large overlap with the samples from the US and Netherlands among the western populations; although, a small overlap with Indian and non-western populations was also noticed. Takahashi, N. & Sato, T. Dipeptide utilization by the periodontal pathogens Porphyromonas gingivalis, Prevotella intermedia, Prevotella nigrescens and Fusobacterium nucleatum. Microbiome https://doi.org/10.1186/s40168-017-0338-7 (2017). We thank the intramural funding received from IISER Bhopal, Madhya Pradesh, India for carrying out this study. Ren, L. et al. Microbial culturomics broadens human vaginal flora diversity: genome sequence and description of Prevotella lascolaii sp. R. Package Version 1.61 (2013). The number of PULs per genome was significantly higher (Wilcoxon rank-sum test, p-value = 0.015) in the differentially abundant Prevotella genomes in non-western populations compared to western populations. Scher, J. U. et al. https://doi.org/10.1126/scitranslmed.aap8914 (2018). Likewise, it was relatively enriched in genes involved in proline, histidine, and lysine biosynthesis, as were the populations from Peru and Tanzania (Supplementary Fig. A significant difference between western and non-western populations was observed based on the number of antibiotic resistance genes identified and the Shannon diversity index (Fig. The immune response to Prevotella bacteria in chronic inflammatory Integr. https://doi.org/10.1038/s41591-019-0406-6 (2019). Differentially abundant VFs in western and non-western were also identified. b Box plot showing the inter-sample distance (BrayCurtis) of Indian samples with other populations based on the relative abundance of genes of PGC.

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