3.3 Profiles of the gut microbiome
The raw sequence count per sample ranged from 3 456 to 234 172 for the gut microbiome samples, with an average sequence count of 58 613 per sample. After the DADA2 process, 1 138 features were reported, with a total frequency of 1 926 036. Frequencies per feature ranged from 2 to 249 452, with a median frequency of 72; feature frequencies per sample ranged from 1 857 to 165 900, with a median frequency of 33 888. By using the trained classifiers based on Greengenes 13_8 99% OTUs (taxonomic assignment based on a 99% similarity), the bacterial taxonomy of the fecal specimens included 11 bacterial phyla and 133 genera. The top dominant bacterial phyla (Figure 1A) wereBacteroidetes , Firmicutes , Proteobacteria ,Verrucomicrobia , and Actinobacteria , whereas the dominant bacterial genera (Figure 1B) included Bacteroides ,Faecalibacterium , Prevotella , Roseburia , andRuminococcus .