Separate compartment. Conception occurs in the Fallopian tubes and the embryonic material migrates to the inside of the womb. There it will attach and develop. Simple bacterial vaginosis is a localized problem within the vagina & the germs involved do not travel up to the areas where the embryo/fetus is beginning to develop. If you eventually treat the vaginosis, baby will not encounter those germs during delivery.
Bacterial vaginosis. No as long as you have been treated and infection clears up, there will be no harm to the baby.