> const input = { ['__proto__']: { a: 42 } }
undefined
> output = bson.deserialize(bson.serialize(input))
{}
> Object.getPrototypeOf(output)
{ a: 42 }

The own named property __proto__ should be preserved as-is, i.e. the output object should have a property with that name just like the input object, and instead keep Object.prototype as its own prototype.