The animals with souls are primarily the companion animals, dogs, cats, and horses, and the cetaceans who are high-level beings to begin with. Invasive predatory pest species, including many insects, rodents, and so on, do not have souls nor do the animals considered as food sources like cows and sheep. Using them as food has our blessing and incurs no karmic penalty. The animals, in effect, are choosing to serve in that way. There is no karmic penalty in ridding your home of pests, however you choose to do so. The only consideration is to avoid unneeded cruelty simply to cause excess suffering. That is an ungodly act, for whatever reason, and it is that intention to cause suffering that is the karmic misstep more so than to what it is directed. So for ordinary housekeeping, you need not worry about something that wanders your way that you dispatch by whatever means, as long as it is not prolonging the death to extend the suffering. Some things simply cannot be helped if there is no practical way to rescue such a creature, but you are in no way obligated to do so, either, for predatory species because they are an intruder in your world to begin with.
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