16S data analysis for low abundant bacteria

Hello, I am inserting tables in txt of tick samples vectors of microbial pathogens, treatment and taxonomy made from 16S v3-v4 amplicons (444 bp) with the dada2 package in R. When importing the taxonomy on the website, I have OTUs/ASVs of interest (pathogens) with low counts, with low richness and abundance. So the graphs and exploratory analyzes filter my data too much and even trying to use the minimum filter, my taxa of interest do not appear. Is there a tool that allows you to include/input all taxa?
I have already confirmed with other genes that they are present in the samples, so even with low counts/abundance for 16S I would like to include them.

You can (seems you already did) turn off the filtering by dragging the sliders to be 0. Then the only filter will be the two steps in Data Quality check

  • Features with identical values (i.e. zeros) across all samples will be excluded;
  • Features that appear in only one sample will be excluded (considered artifacts);

These two are minimal filtering and should always be performed (I don’t see any reasons not to do it). There is no other filtering steps as far as I am aware. I wonder what makes you think the tool has filtered your data?

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Thanks for the answer, jeff.xia. As you said in the answer, it seems to me that some OTUs/ASVs sequences must be considered artifacts, since in only one of the samples from one of the treatments I have the taxon of interest (and in low abundance). I still don’t know how to get around this data entry to also consider these sequences, since by sequencing another gene I confirmed the presence of the same taxon in that sample.