Do the microbes that live on our bodies cause heart disease and autism?

DEAR DOCTOR K: You recently wrote that the microbes that live on and within us might be a cause of disease. A friend told me she heard they might cause heart disease and autism. Is there any truth to that?
DEAR READER: For a long time we've known that defects in how our genes are built, and defects in whether our genes are appropriately turned on, powerfully influence whether we develop diseases. However, our human genes may not be the only genes that affect our health. Trillions of germs live on and within us, all of our lives. They live on our skin, in our mouth, in our gut and elsewhere. And they have genes, too. We call their genes, collectively, our "microbiome." Indeed, our microbiome contains about 400 times more genes than we have human genes.