"Inside John Barth" by William W. Stuart, first published in the June 1960 Galaxy. You can read the Project Gutenberg etext.
Don't remember the exact start to the story, but it went something like "walking along a path" or something, and when he hears what sounds like a shotgun blast behind him, he then feels something strike him in the butt.
We were lounging by the campfire after supper and a few good snorts. Uncle John was entertaining himself with a review of some of his nearer, more thrilling misses. I, to tell the truth, was sort of dozing off.
Then, all of a sudden, there was a bright flash of blue-green light and a loud sort of zoop-zing sound. And a sharp, stinging sensation in my thighs.
I hollered. I jumped to my feet. I looked down, and my pants were peppered with about a dozen little holes, like buckshot. I didn't have to drop my pants to know my legs were, too. I could feel it. And blood started to ooze.
I figured, of course, that Uncle John had finally shot me, and I at once looked on the bright side. I would be a cinch for a fast promotion to vice-president. But Uncle John swore he hadn't been near a gun. So we guessed some other hunter must have done it, seen what he had done, and then prudently ducked. At least no one stepped forward.
He passes out, and when he awakens, he discovers that the "shotgun blast" was actually a miniature spaceship that exploded and shot miniature aliens into his body.
He doesn't pass out. He does start noticing the beneficial effects soon after the incident, but it's months later when he realizes he has been invaded, after listening to a bar conversation about UFOs:
All at once, standing there on the sidewalk outside Perry's Bar, I knew that it was true. Space invaders. The Earth was invaded—the Earth, hell! I was invaded. I didn't know how I knew, but I knew all right. I should have. I was in possession of all the information.
The aliens prove to be very beneficial because they clean up all the toxins and other poisons in his body.
Communication is established:
"Citizens of Barthland."
"Invaded! Good Lord, of all the people in the world, why me? Nothing like this ever happened to anyone. Why did I have to be picked to be a territory—the first man to have queer things living in me?"
"Oh, please, gracious Fatherland! Permit us to correct you. In the days of our fathers, conditions were, we can assure you, chaotic. Many horrible things lived here. Wild beasts and plant growths of the most vicious types were everywhere."
"What you would call microbes. Bacteria. Fungi. Viruses. Terrible devouring wild creatures everywhere. You were a howling wilderness. Of course, we have cleaned these things up now. Today you are civilized—a fine, healthy individual of your species—and our revered Fatherland. Surely you have noted the vast improvement in your condition?"
They can be transmitted through kissing or sexual activity.
Yep. After his date with Helga:
Back in my apartment—my big, new, plush apartment—I sat down to go over the thing with the Department of the Interior. The enthusiastic response I got surprised me. "Magnificent," was the word. "Superb. Great!"
Well, I thought myself that I had turned in a pretty outstanding performance, but I hadn't expected such applause. "It is a first step, a splendid beginning! A fully equipped, well-armed expedition will have the place settled, under cultivation and reasonably civilized within a day or two, your time. It will be simple for them. So much more than in your case—since we now know precisely what to expect."
I was truly shocked. I felt guilty. "No!" I said. "Oh no! What a thing to do. You can't!"
"Now, now. Gently," they said. "What, after all, oh Fatherland, might be the perfectly natural consequences of your own act?"
"What? You mean under other—that is—"
"Exactly. You could very well have implanted a new life in her, which is all that we have done. Why should our doing so disturb you?"