Surprisingly, the relative abundance of the phylum Verrucomicrobia is 86% in sample X. Only 1 ASV account for the majority of the ASVs classified as this phylum in that sample. This one ASV is classified as Akkermansia (confidence level 92%) and its relative abundance is 84% in sample X. While this ASV is present in 94 samples (out of about 300 samples), the relative abundance of Akkermansia does not exceed 28% in any of the other samples. Interestingly, there are 55 ASVs classified as Akkermanisa (albeit, with confidence levels as low as 72%). This particular ASV is the most prevalent and most abundant among all ASVs classified as Akkermanisa in nearly all samples in which it is present. Surprisingly, sample X has 50 out of 55 of the ASVs classified as Akkermanisa present in the sample, whereas other samples have at most 2 present.
Based on the unweighted unifrac emperor 3D plot, sample X looks like an outlier, but not based on the weighted unifrac emperor plot. I haven’t found anything abnormal about the sample itself other than this issue. It looks like the sample has a normal taxa profile by presence although by relative abundance, all other taxa in the sample are smaller by percentage relative to the other samples (See the figure below. Sample X is the last column, ordered by Verrucomicrobiae abundance in ascending order). This sample has 322 representative ASVs and 226,603 total sequences, both above the median by about 1 and 2 standard deviations, respectively. I ran the Deblur alternative pipeline and everything seems to have run well, there wasnt any major loss of reads in any of the pipeline steps. Quality of the sample looks good (checked using fastqc). Mock communities look good. Reads are from the V4 region of 16S rRNA and classified using my trained SILVA taxonomy. Its Bristol Stool scale type is 3, which is considered normal by the scale. The person was not treated for anything recently but was on medication. However, other participants were on the same medication and none of them had this extreme overgrowth.
Any ideas why there is an extreme overgrowth of Akkeremansia strains in this one stool sample? Have you seen something like this before? Could this be a technical issue? Your thoughts are much appreciated.