4 1.22 3.99 3.63 0.03 Clostridium hathewayi 1.31 3.01 0.98 1.49 0.26 Clostridium phytofermentans 3.04 2.68 2.6 5.65 0.02 Clostridium proteoclasticum 0 1.13 3.65 0.66 0.83 Dialister invisus 1.53 0.44 3.15 2.83 4.02 Eubacterium rectale 3.44 2.13 2.39 2.79 0.43 Faecalibacterium prausnitzii 5.99 2.45 6.02 8.1 9.4 Oribacterium sinus 0.31 2.18 0 0 0 Roseburia inulinivorans 4.17 0.97 1.99 4.43 1.52 Salmonella enterica 0.69 0.44 1.24 0.78 6.15 unclassified
24.44 6.48 22.09 9.72 22.87 Xenorhabdus nematophila 0 0 0 0 4.5 The most abundant species associated with each KO within the Doramapimod datasheet peptides/nickel transport system are shown here. The five most abundant species in each KO are highlighted in bold find more and also listed for every other KO. Analysis of Faecalibacterium prausnitzii strains within reference protein phylogenetic trees The probable origin of each subunit of the peptides/nickel transport system within F. prausnitzii PF-6463922 research buy was examined using full-length protein trees derived from 3,181 sequenced species. It was found that the five sequenced strains of this species (M21/2, A2-165, KLE1255, SL3/3 and L2-6) contained up to 6 copies of each gene, which were spread across up to six operons with an average of 2.8 per strain (Figure 2). Operons were classified based upon whether the strains formed a closely
related group within the full protein tree of the constituent KOs. Up to six such groups were found within each protein tree for K02031-K02035, resulting in the postulation of six operon types, each with a potential separate origin. Each operon type appeared to be derived from an LGT event from strains of various taxonomically spread species (Additional file 4: Figure S3). However, most of these species are associated with the human gut microbiome, suggesting that habitat-direct LGT occurred. Operon 3, which is complete only in strain A2-165, appears to have been potentially acquired from multiple bacterial IMP dehydrogenase species with the ATP-binding proteins (K02031 and K02032) separately acquired from the remaining proteins (Additional
file 4: Figure S3). Gene neighbourhood analysis revealed preservation of operon organisation between F. prausnitzii strains and potential donors of operons, though not similarity in flanking regions, adding credence to the possibility of LGT resulting in acquisition of this function. Although multiple strains of F. prausnitzii contain each type of operon, suggesting acquisition prior to strain separation, rearrangement of the gene constituents appears to be frequent with inversions observed in operon types 2 and 5 and potential loss of components in operons 3, 4, 5 and 6 (although sequence similarity between missing sections of operon 5 in strains A2-165 and L2-6 and K02035 indicate this gene is present, though not annotated correctly). Figure 2 Arrangement of peptides/nickel transporter operons within the five strains of Faecalibacterium prausnitzii.