Are there any references to microbes, such as bacteria or viruses, in any Hindu scripture?
Microbs in Hinduism scriptures.
Yes , there is mentioning of microbes in Hinduism Scripture. Take a look at below verse from Shanti-Parva of Mahabharata -Section XV.
The word krimi (कृमि) is generally used in for such microscopic creatures like bacteria ,virus or other tiny worms almost invisible to human eye. Here in below verse the word Sukshma Yoni(सूक्ष्म-योनि) is used to mention microscopic organisms.
Here in this chapter Arjuna is talking about the concept of "Survival of the fittest" , which modern science stated thousands of year later on.
सूक्ष्मयॊनीनि भूतानि तर्क गम्यानि कानि चित |
पक्ष्मणॊ ऽपि निपातेन येषां सयात सकन्धपर्ययः||
P.26 There are many creatures that are so minute that their existence can only be inferred. With the failing of the eyelids alone, they are destroyed.
Although there is just mentioning of these microbes in Mahabharata and no other details are given ,but because it's not the main topic and even not in the scope of religious Scripture. But it's sure that the verse is talking about these microscopic organisms which gets destroyed or die within time required to close-open eyelid.i.e. very short lifespan.