(Below N is a link to NCBI taxonomic web page and E link to ESTHER at designed phylum.) > cellular organisms: NE > Bacteria: NE > FCB group: NE > Bacteroidetes/Chlorobi group: NE > Bacteroidetes: NE > Bacteroidia: NE > Bacteroidales: NE > Prevotellaceae: NE > Prevotella: NE > Prevotella copri: NE > Prevotella copri DSM 18205: NE
Warning: This entry is a compilation of different species or line or strain with more than 90% amino acid identity. You can retrieve all strain data
(Below N is a link to NCBI taxonomic web page and E link to ESTHER at designed phylum.) human gut metagenome: N, E.
Prevotella copri CAG:164: N, E.
uncultured bacterium: N, E.
uncultured bacteria: N, E.
Prevotella copri: N, E.
LegendThis sequence has been compared to family alignement (MSA) red => minority aminoacid blue => majority aminoacid color intensity => conservation rate title => sequence position(MSA position)aminoacid rate Catalytic site Catalytic site in the MSA MKLKRHLLTAALTLFCLSAANAQLLRTTVEQGEIEGVEHEGFALYKGIPY AEAPVGNLRWKAPVSKKPWKGVFKADKWGDRPPQPIDPNQNGGEQGMSED CLYLSVETPAKSKNDKLPVFVMIHGGAFLTGSYSGTQESFVKEGIIYCSI EYRLGALGFMAHPELSKESGKNISGNYGILDQVMALKWIHDNIAAFGGDP DKITIAGESAGGISVSILCASPLAKGLFRGAISESGSSFWPVGESRNGNT AMLTSKAAEAGGLLLQKRLKAKNLKQLRKVPAMDIVKNTAFESFWPNVDG YSITDDQYKLYEKGSYNDVNVIIGTNSDEGSMFSRPVSVSDYEKRIHEIY GSWADQVLSLYPARTEEETYFAQSDIFRDGSFAWGTYAWANLQSKTGKGK VYMYYFDQDSENTIVKSRKGGASHVAEMPFIYGYKFGSGKMTETEQHMEQ IMSRYWINFTKTGNPNGDSLPFWTTYQEGKPTVMIMKEGLHLGPVQNQKQ MDFFEKFFKEKRK
Metagenomic approaches are widespread in microbiological research, but so far, the knowledge on extrachromosomal DNA diversity and composition has largely remained dependant on cultivating host organisms. Even with the emergence of metagenomics, complete circular sequences are rarely identified, and have required manual curation. We propose a robust in silico procedure for identifying complete small plasmids in metagenomic datasets from whole genome shotgun sequencing. From one very pure and exhaustively sequenced metamobilome from rat cecum, we identified a total of 616 circular sequences, 160 of which were carrying a gene with plasmid replication domain. Further homology analyses indicated that the majority of these plasmid sequences are novel. We confirmed the circularity of the complete plasmid candidates using an inverse-type PCR approach on a subset of sequences with 95% success, confirming the existence and length of discrete sequences. The implication of these findings is a broadened understanding of the traits of circular elements in nature and the possibility of massive data mining in existing metagenomic datasets to discover novel pools of complete plasmids thus vastly expanding the current plasmid database.
Recent research has disclosed a tight connection between obesity, metabolic gut microbial activities and host health. Obtaining a complete understanding of this relationship remains a major goal. Here, we conducted a comparative metagenomic and metaproteomic investigation of gut microbial communities in faecal samples taken from an obese and a lean adolescent. By analysing the diversity of 16S rDNA amplicons (10% operational phylogenetic units being common), 22 Mbp of consensus metagenome sequences (~70% common) and the expression profiles of 613 distinct proteins (82% common), we found that in the obese gut, the total microbiota was more abundant on the phylum Firmicutes (94.6%) as compared with Bacteroidetes (3.2%), although the metabolically active microbiota clearly behaves in a more homogeneous manner with both contributing equally. The lean gut showed a remarkable shift towards Bacteroidetes (18.9% total 16S rDNA), which become the most active fraction (81% proteins). Although the two gut communities maintained largely similar gene repertoires and functional profiles, improved pili- and flagella-mediated host colonization and improved capacity for both complementary aerobic and anaerobic de novo B(12) synthesis, 1,2-propanediol catabolism (most likely participating in de novo B(12) synthesis) and butyrate production were observed in the obese gut, whereas bacteria from lean gut seem to be more engaged in vitamin B(6) synthesis. Furthermore, this study provides functional evidence that variable combinations of species from different phyla could 'presumptively' fulfil overlapping and/or complementary functional roles required by the host, a scenario where minor bacterial taxa seem to be significant active contributors.
