Prior to the 20th century most people lived around farm animals and even "city folks" lived in close proximity to horses and were just used to the stench. It's only with the advent of modern hygiene that it comes as a shock when we are reminded of our animal origins.
But I've never heard of a time travel story where travelers found themselves gasping for breath as soon as they entered a room filled with a native crowd. Would make a good short story. :)
Read the Outlander series. The stink of the room or crowd is often mentioned by Claire the time traveler.