I would first assume that bacteria has not been totally eliminated, as total elimination is not something easy to do. A small remnant colony may still exist.
The problem with certain antibiotics is that they can lead target bacteria to morph into a form that is more resistant in the form of cell wall deficient bacteria. When not dependent on having a cell wall to survive, these bacteria are more resistant and more virulent, and can lead to a microbiome where fungal forms increase their dominance.
This leads further to the loss of balance in the microbiome and more dysbiosis and opportunities for infection.
Use of natural substances available in nature that are known for their antifungal properties may help as a start. Taking turpentine orally, for example. This would help change the microbiome towards a dominance by bacteria instead of fungal forms.
I believe many diseases attributed to putative viruses are simply fungal forms, as something said to be invisible bears the stigma of mystery, and mystery always carries with it the fear of the unknown, of which snake oil doctors like to engage in for their business of parasitism of the masses of fearful and superstitious masses.
Another avenue worth exploring is aromatherapy, on the use of essential oils, especially use of suppositories with blends tailored to fit the suspected pathogens in play. Since essential oils are composed of primary and many secondary metabolites, they have various pathways of action that make them much less subject to pathogenic resistance, in contrast to the single mode of action of antibiotics, which pathogens can easily build resistance to.
Of course, there is the use of fecal transplants but this is one I would consider only out of desperation. I would rather that I share a glass of water with my pet cat or dog, in the hope that I can get some of the bacteria from them. But if the bacteria I want is an obligated anaerobe, it would be hard to obtain that bacteria this way.
