As I understand, some of the microorganisms are pathogenic. Thus we can conclude which farm is better to develop and which one to close. Also, the density of fish population should be reduced.

Several factors influence gut microbiota including, age, diet, culture water, temp are critical ones. Depending on differences in immune and physiological responses, even same species of same age and sex can have differences in gut microbiota. So it is not surprising to find differences in the diversity of gut microbiota in the same fish species raised in different farms.

Two different location is important. Either it is lentic or logic. Either it is from fresh water or from marine water. Either it is from fresh water or estuarine or brackish water. According to location fish gut microbial growth may differ. Mainly E.coli population and other microbes and cocchi and virgo colerea may found in fish gut.

According to my understanding of this is that; Although the fish are of the same species, there's kind of bias introduced when they are grown from different locations. You cannot expect to find similar microbial communities in the guts of these fish in regards to different environmental factors that may affect the presence and abundance of the microbes, leave alone the fact that immune responses differs from one individual fish to another even if they belong to the same species

To conclude your study you can identify the sources of specific microbiota on a specific population with their feeding habit. The ranges of microbiota vary with feeding zone and water quality.