SKIN, GASTROINTESTINAL AND RESPIRATORY TRACT
There are a lot of microbes (bacteria, viruses, fungi and parasites) as part of normal flora in healthy people, especially on the skin, in the upper respiratory tract and in the lower gastrointestinal tract.
Microbes can enter the body through mouth during birth, when travelling from the vaginal canal or, later, by breathing and with food.
You can also find microbes in other healthy tissues, where you might not expect them.
Helicobacter pylori in normal gastric mucosa (PubMed, 1994):
Several Western studies have shown prevalence of H. pylori in normal gastric mucosa to range from 0-25%.
Pneumocystis carinii, Medical Microbiology, 4th Edition (NCBI, 1996):
In normal individuals, asymptomatic infection of the lungs occurs in early life.
NERVES and BRAIN
After chickenpox infection, some Herpes viruses travel along the nerves and may remain dormant in the dorsal root ganglia of the spinal nerves...they can be activated later and cause shingles.
According to (jvi.asm.org):
Herpes simplex virus 1 (HSV-1) establishes latency in neurons of the brains and sensory ganglia of humans and experimentally infected mice.
INTERVERTEBRAL DISCS
Our findings further validated the presence of low-virulence anaerobic bacteria in degenerated IVDs, and P. acnes was the most frequent bacterium.