How does the microbial environment in your gut initiate?
The initiation of gut flora come from maternal cervical and vaginal flora (Bezirtzoglou, 1997)1. These predominantly include facultative anaerobes (e.g., Staphylococcus, Enterobacteriaceae and Streptococcus). Birth by caesarean section can cause problems because these bacteria are not passed on in the  usual manner.

Vael et al. (2011)2 found an association between early gut flora and obesity later in life


  High intestinal Bacteroides fragilis and low Staphylococcus
  concentrations in infants between the age of 3 weeks and 1 year were
  associated with a higher risk of obesity later in life.


suggesting that monitoring or alterations of gut flora might be effective in reducing rates of obesity.

Bezirtzoglou E. 1997. The intestinal microflora during the first weeks of life. Anaerobe 3:173-177.

Vael, C., Verhulst, S.L., Nelen, V., Goossens, H., Desager, K.N. 2011. Intestinal microflora and body mass index during the first three years of life: an observational study. Gut Pathog 3: 8.