I think the number one thing is stay away from antibiotics, for both you and baby. If you're GBS positive, look into other ways of reducing/eliminating the bacteria in your body (the pregnancy and birth boards have a lot of threads on this).
I personally don't think low-carb a la Atkins is healthy, esp. while breastfeeding (see www.kellymom.com
for more information) but I definitely think it's worthwhile to cut out "white" foods - white bread, white pasta, potatoes, sugar, and focus your carbs on healthy complex carbs like whole grains, beans, fruits and veggies.
It's also good to make sure that your system is full of healthy probiotics - the beneficial bacteria in your gut. A good probiotic supplement can be healthful, as is eating yogurt and drinking kefir (just stay away from the sweetened varieties if you buy them - making your own is a good way to get probiotics too).
If you have a homebirth your baby's gut is more likely to be colonized with beneficial bacteria from your system. But if you have a hospital birth make sure baby gets no formula and feed baby some probiotic powder designed for babies (just wet your finger a little with breastmilk and put some powder on it, then let baby suck your finger).