Aza shares with the reader that the human body is made up of about 50% bacteria; essentially, half of a person's cells aren't technically that person. Aza's OCD makes this knowledge unbearable for her and she's obsessed with keeping herself as clean and bacteria-free as possible. The way she conceptualizes bacteria as controlling, invasive, and malicious symbolize a literal split in Aza's identity: the bacteria provide Aza proof that her identity is not her own.
Bacteria (C. diff) Quotes in Turtles All the Way Down
... and meanwhile I was thinking that if half the cells inside of you are not you, doesn't that challenge the whole notion of me as a singular pronoun, let alone the author of my fate?
His bacteria would be in me forever, eighty million of them, breeding and growing and joining my bacteria and producing God knows what.
It was saying that my bacteria were affecting my thinking--maybe not directly, but through the information they told my gut to send to my brain. Maybe you're not even thinking this thought. Maybe your thinking's infected.