We studied the antifungal activity of some plant extracts in vitro against the known standard strains of fungi. However, we did not perform in vivo experiment.
You first try to get the standard strains of bacteria and fungi to conduct in vito assay of plant extract. If the results are encouraging, you can go for in vivo studies on laboratory animals after obtaining ethical clearance from the authority.
The main concern is that an extract may be not just antimicrobial but antiseptic, killing everything. Your first hint will be when it kills both bacteria and fungi. You should plan to counterscreen for toxicity to a mammalian cell line in culture.
One method is to treat a culture of cells, such as an immortalized human cell line (e.g. A562), with a set of serial dilutions of the extract in a 96-well microplate for a day, then measure the metabolic activity of the cells using a tetrazolium dye assay.
We studied the antifungal activity of some plant extracts in vitro against the known standard strains of fungi. However, we did not perform in vivo experiment.
You first try to get the standard strains of bacteria and fungi to conduct in vito assay of plant extract. If the results are encouraging, you can go for in vivo studies on laboratory animals after obtaining ethical clearance from the authority.