No, it will not. Fully cycled aquariums typically make it through treatment with NeoPlex™ with no impact on the beneficial bacteria colonies at all.
It is worth mentioning, though, that NeoPlex™ (like most medications) will slow down the growth of new beneficial bacteria colonies. That means that a tank being treated with NeoPlex™ will be slower to "spring back" after a major disturbance or bacteria die-off, and new aquariums will be significantly slower to cycle. While treating with this or any other medication, Seachem® recommends paying close attention to maintaining stable water parameters and dosing a bacteria supplement like Stability® or seed™ as needed to help the biological filtration recover from water parameter fluctuations. You can also avoid touching the bacteria colonies in the tank entirely by using NeoPlex™ in the fish's food instead of dosing it directly into the water.
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