They are always harmful but never beneficial or neutral.

Viruses

Explanation:

All viruses are pathogenic.

Bacteria, if not pathogenic, they could be neutral or even beneficial. Eg: our intestinal flora are capable of producing Vitamin K and most of the Vitamin B complex. They also compete with other bacterial species that could be pathogenic and don't allow them to reach harmful levels.

They don't harm us and are called commensals.

Fungi are usually neutral commensals that normally live in our body until you become immunodeficiet. They might then become pathogenic.

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