Why do microbes in our gut form a certain structure? Why do not they overgrow? Are there some limiting factors of their growth? Such as the source of C, N and P, oxygen availability, host immune or others?
On eof the major aspects controlling the bacterial equilibrium would be the presence of commensal Entamoeba that feed on bacteria.
Generally the stomach is known to be the first line of defense against bacteria. This is due to the the gastric fluid which generally provides unfavourable acidic conditions that dont allow the bacteria to proliferate. Also gut has lactoferrin which also prevents certain microbes from growing. The microbes that are able to pass through the gut and grow are known have ceratin tolerance or resistance mechanisms that allow them to survive and adapt to these harsh conditions.
The stomach is an environment which has specific organisms that colonize it and these outcompete the unfavorable ones. Other aspects such as pH, food taken also contributes to the microflora community in that unique environment.
Here is a good paper reviewing how interactions between the host and commensal microbiota might regulate the composition and growth of gut microbiota.
http://www.sciencedirect.com/science/article/pii/S0952791510000968
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