Isaac, I think your samples are well below the Nyquist rate.

Normal Gut Transit Time is on the order of one to two days, your microbiome can also change rapidly, and the growth rate of Foodborne Illnesses can be as fast as 8 hours. You may also see changes over the length of a stool sample given that it represents multiple meals of different foods and give consideration to surface or interior sampling. There are also other factors such as exercise and stress that may change your results. Even how long the sample was exposed to oxygen may have an impact.

You could improve the measurements, but that would take some real dedication and $$$. Setting up a two level Design of Experiments test with daily sampling over a month. Eating the same food for all meals in a day (bracket your sample with the same food). Ingesting a non-toxic marker to know where to sample on the stool…

Then you get to what to do with the results. It may be that diversity is better than boosting the concentration of a specific family of microbes. One potential source of information on your microbiome is the American Gut Project.

Good luck.