In general, Firmicutes were the dominant phylum associated with each KO, as is to be expected by their abundance within the gut , with the class Clostridia and
order Clostridiales making up the largest proportion of classified reads in each sample. Several Firmicute genera, including Clostridium, Blautia, Ruminococcus and Faecalibacterium, were found to be in relatively high abundance in almost every protein set (up to 15%). Members of other phyla such as Proteobacteria and Actinobacteria also contributed to the species composition of proteins within this complex though these signals were less abundant and consistent than the Firmicute members. Thus, although correlation of assignments at higher taxonomic selleck chemicals ranks
was found between KOs, this did not extend to the genus level. This could be due to incorrect taxonomic GDC-0449 solubility dmso assignments as a result of a deficiency in relevant reference genomes or lack of predictive power from the metagenomic ORFs. Inconsistencies could also be due to recent LGT events between members of different genera, which would result in discordant taxonomic assignments associated with the recipient species. Thus it is possible that this protein complex is present in a smaller, more consistent, set of genera with the human gut microbiome than is observed here. Table 1 Percentage of reads assigned at each taxonomic level for each protein in the peptides/nickel transport system KO Phylum Class Order Family Genus Species K02031 98.11 96.61 96.36 91.1 84.71 75.56 K02032 99.68 99.45 99.26
98.06 96.2 93.52 K02033 98.61 97.9 97.3 93.28 83.68 77.91 K02034 Y-27632 2HCl 99.64 99.54 99.32 97.9 95.61 90.28 K02035 98.21 94.93 94.62 86.84 84.35 77.13 Mapping of species classifications revealed further disparate signals between the KOs. Within each of the proteins K02031-K02035, no single species was represented in more than 9% of taxonomic attributions (Table 2). Collectively, the top four contributing species did not comprise more than 25% of the taxonomic groups associated with any of these KOs. As many of the fragments were not classified to the species level (average of 17.12%), it is difficult to determine exactly what species are most commonly associated with each protein. Analysis of the peptides/nickel transport system revealed very little overlap in species composition between the individual proteins of the complex. Only Faecalibacterium prausnitzii was found in relatively high abundance in all five KO phylogenies, with most other highly abundant species only being highly associated with at most three components. However, all of the most abundantly associated species are resident within either the gut or the oral cavity of the human microbiome. Thus, despite low overlap of species composition, fragments were found to be derived from microbes associated with the human alimentary canal as is to be expected.