I have not understood the role of antibiotic medium in filtering the bacteria containing the recombinant plasmids with the ones having normal plasmids. Since all the plasmids of a certain bacterial species have a antibiotic resistance gene regardless if its recombinant or not , shouldnt there be no effect of the antibiotic on the colony?
Short answer: selection protocols are designed to work
When choosing a selectable marker for a plasmid, one chooses a gene that is known to be absent in the host organism of interest. For example, standard lab strains of E. coli are free from extragenomic plasmids and are susceptible to the antibiotic ampicillin. As such, plasmids that confer resistance to ampicillin are commonly used to maintain plasmids in E. coli lab strains.
Other things worth noting:
1. Antibiotic resistance genes are not universal.
That is, a bacterial strain that has a gene imparting resistance to one antibiotic may still be susceptible to many other antibiotics.
2. Not all plasmids carry antibiotic resistance genes.
Many naturally occurring plasmids are selected for in the wild because they carry genes that enable the bacteria to perform new metabolic functions, or impart virulence genes that enable bacteria infect a host organism: (https://en.wikipedia.org/wiki/Plasmid#Properties_and_characteristics). This is also true of recombinant plasmids. Many commonly used yeast plasmids are selected for by enabling the host strain to produce a necessary nutrient that is absent in the growth medium.