Can 16s sequencing of my intestinal bacteria identify any/all of following infections: h. pylori, c. jejuni, toxoplasma gondii?

Yes but...: Dna sequencing can identify most of the bacteria and also the % of those present. What you are going to use this for is perhaps the most important question and where are they located? I would check with your physician, find out what testing facility they are using and how extensive is the test. Some of the test only look for a few of the bacteria and don't measure them all.