Exactly - the two most important things are your research experience and your LoRs.
@B77729 At the moment, your GPA is on the low side, which may be what is keeping your from being interviewed - often there is a quick triage, and applicants with low GPA and/or Low tests scores are put aside.
That is a major reason for you to reach out to potential advisors. When you reach out to potential advisors, it is an opportunity to make a good impression, and get them to see you as a potential students, not as another name on an application. If you have a PI who likes your profile and is interested in having you join their lab, they will make sure that your profile gets through the first cull. That is where your research experience and LoRs kick in.
Back in the Stone Age, when I was applying to PhD programs, I had a masters, some good publications, great LoRs, a good GPA, and great GRE scores. However, my application languished until the person I contacted, and who was interested in recruiting me, got back from a vacation and started pushing my application.
Another issue may be your undergraduate institution. Unfortunately, academia can be prestige-ridden, and your alma mater can affect your chances of being accepted.
Another important issue is that you did not know whether any of your potential PIs was even recruiting graduate students. I mean, if you were interested in, say, DNA transfer between bacteria, and none of the people who are working on that were looking to add a graduate student to their lab, your application would definitely no longer be considered.
If the problem is either your GPA or your alma mater, doing a masters would be a good idea. I would normally advise that you go and get a job as an alternative. However, since your degree is in microbiology, only do so if you can engage in some level of research in your job. If you will be doing the most basic tech work, it’s not all that helpful.
The question is - can you afford a masters? Many are not supported, so you would have to pay out of pocket.
In any case, I would advise you to first reach out and meet with potential advisors and see what they say. It is obvious that your PI was giving you incorrect advice, and their other advice as to where you should apply, what your application looked like, etc, may have been incorrect as well. Meeting with potential PIs and seeing how they respond will help you have a better idea as to how strong your application is, and whether it would benefit from some more years of work or a masters.