Bacteria are in virtually all parts of your body — your face, genitals, underarms, bowel, lungs . . . they make up the biomes of each organ system, your skin among them.

My fascination with bacteria began as a high school student, when I spent weekends growing them at a local hospital and volunteering in the bacteriology laboratory. Viruses were dead, and most hospitals cannot grow them.

Bacteria seemed to have lives of their own. They had character, color in some cases, odors, and growth characteristics which assisted in their recognition and identification. They could degrade plastics, oil, and flesh. They had survived in the coldest and hottest places on earth. They colonized human organs and delivered us energy, heat, foods, drinks, and much more.

Billions of years ago, bacteria became part of each of our cells in the form of an organelle (little organ) called a mitochondrion. Life is impossible without these mitochondria, and I along with others believe that they are at the source of some of our diseases. They also inform our immune systems. Each mitochondrion is inherited solely from our mothers’ eggs and are a vestigial bacterium replete with its own DNA. (Vestigial in the sense that they are vestiges of a prehistoric infection.)

Our bodies have billions of these mitochondria powerhouses. They generate energy in the form of adenosine triphosphate (ATP), a chemical current of sorts, which is essential for every energy consuming activity that we have. The attributes these bacteria give us while growing in our biomes, skin, lung, bowel, and kidney provide our biological soul with continuing education of a sort and are probably the greatest single source of clues to the causes of our most devastating diseases.

But beyond the mitochondria and friendly invaders lurk some nasty ones.

Consider Lyme disease, a common tickborne illness caused by the bacterium Borrelia burgdorferi. Lyme results in flu-like symptoms, rash, fatigue, and joint pain and weakness and — as with all bacteria — the chance for cross-reaction with other diseases. Lyme relies on the immune system for clearance of its spirochete, the Borrelia. Spirochetes are a class of bacteria that include the bad (Lyme, syphilis) and harmless (those found every day in our mouths).

After all, all criminals have families; some who are criminals themselves, some completely innocent. In the case of Lyme, the body is invaded by the spirochete, which is eliminated by the immune system but not before the immune system, seeing spirochetes in certain organs like the joints, keeps ravaging the body as though the bug was in the blood.

Depending on the stage of the disease, Lyme can be eliminated from the body with adequate treatment over a few weeks, but the immune system can continue to provide symptoms, which are exceedingly difficult to treat.

This difficulty has been compounded by a bit of controversy: With initial descriptions of Lyme disease, countless doctors and pharmacies spent months treating patients for the bacterium rather than realize that they were looking at what the immune system was doing to their patients. But they did it late, and the ongoing use of antibiotics for up to six months in some patients made no sense. The Lyme was gone.

Huge, unnecessary antibiotic bills from medical practices with a total lack of understanding about Lyme disease is another reason why understanding the nature immunity is so important.