You have to separate your physics simulation (bodies) from the graphical representation of the physics world.
Lets assume you have a Box2d body defined like this
CircleShape shape=new CircleShape();
FixtureDef fd = new FixtureDef();
fd.shape = shape;
BodyDef bd = new BodyDef();
bd.type = BodyType.DynamicBody;
Now in the render() method your first step the physics world
Then you draw your body
Vector2 pos = body.getWorldCenter();
float angle = body.getAngle(); //if you need rotation
shapeRenderer.circle(pos.x, pos.y, radius);
The same goes for all bodies (static and dynamic) in the physics world you want to render.
Of course you have to set up the physics world, camera and so on properly first.