What is the justification for bacterial vaccines for which the body has natural immunity?
What is the purpose of using vaccines against commonly found bacteria? Since the human immune system develops at birth and shortly thereafter (via colostrum) natural defenses against common bacteria, presumably the body already has antibodies against common bacteria. What purpose is there in "innoculating" someone against such bacteria?
For example, bacteria like pneumococcus endemically colonize everyone's lungs. In one study pneumococci were found in 80% of the healthy patients studied. Of course, that is just the bacteria that were found. Undoubtedly the other 20% of the healthy patients had various colonies of pneumococcus which simply went undiscovered. So, obviously the human body is well adapted to constantly defend against pneumococcus, yet there are varieties of pneumococcal vaccine anyway. Why would this be? To make money, or is there a proven biological action that implies a benefit? By a "biological action" I mean an explanation of the immunological mechanism by which the innoculation significantly augments pre-existing T-cell/B-cell receptors for common bacteria such as pneumococcus, and has a real benefit which is not merely reduplicative.
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There are two immune responses to an infection, primary and secondary. Vaccination makes it possible for the body to immediately switch to a secondary response. So that's why young adults are vaccinated again meningococcal disease so that they don't die from meningitis while the body is still mounting its primary immune response.
The secondary immune responses can usually prevent disease, because the pathogen is detected, attacked and destroyed before symptoms appear. In general, adults respond more rapidly to infection than children. They are able to prevent disease or reduce the severity of the disease by mounting a rapid and strong immune response to antigens they have previously experienced. In contrast, children have not experienced as many antigens and are more likely to get sick.
Memory of the infection is reinforced and long lived antibodies remain in circulation. Some infections, such as chickenpox, induce a life-long memory of infection. Other infections, such as influenza, vary from season to season to such an extent that even an adult is unable to adapt.
www.immune.org.nz/immunisation/immune-system-vaccination
As @BryanKrause points out in a comment, there are many, many, strains of Pneumococcus, many of which do not cause disease in otherwise healthy humans. The paper you referred to looked at 500 strains of Pneumococcus: "They formed smooth colonies and were for the most part avirulent for mice." That is, most of the strains they looked were not disease causing! You may be more familiar with this phenomena with E. coli and food borne disease. All of us have guts full of E. coli which we live in a symbiotic relationship with. However, if you pick up the wrong strain from a contaminated salad bar, you can get very, very, sick.
For bacteria, the species level is a fairly gross classification, and each strain may have subtle variations in the proteins presented at the surface of the bacterium. These surface proteins can play a key role in both the virulence of the bacteria, and our immune response to it. The CDC tracks 90 strains of Pneumococcus that are responsible for most serious human disease. The current pneumococcal polysaccharide vaccine is effective against 23 of those strains.. Having been exposed to one of the non-disease causing strains does not necessarily confer immunity to a disease causing train. It depends on the details of the differences between the strains.
In addition, our immune systems tend to fail as we get older. As we age our immune systems have a lessened ability to respond to new infections, and they can even "forget" how to respond to pathogens that have already been seen. That's why the CDC recommends this vaccine for adults over the age of 65, and younger adults with compromised immune systems. It isn't generally offered to healthy young people.
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