Group B Strep

This is my first pregnancy (I'm 10 weeks 6 days today) and due on October 8, 2016.  All of my prenatal tests have been normal so far except for Group B Strep from a urine test. My doctor started me on a weeklong course of antibiotics and said I will need an iv during labor.  Has anyone else gone through this?  Will the antibiotics prevent/kill the microbiome?  Obviously I am trusting my doctor, but I am so nervous (even though I know this is a relatively common thing). Thank you so much!