Microbes developed interactive signalling systems over billions of years. Scientists do not have a complete grasp on how antibiotics are produced or what they do in the natural world. There are several theories that involve gene transfer, evolutionary selection, and competition. At first it was believed that microbes produced antibiotics when competing microbes encroached on their territory, but this explanation was proved wrong when microbes began producing antibiotics in a laboratory setting with no other microbes present.
Recently it has been demonstrated that in small doses, antibiotics affect the DNA of their intended targets, giving scientists reason to believe that what we have termed “against life” are actually life-sparing signals that don’t kill, but “convince.” At high, pharmacy-grade, therapeutic doses, though, this convincing is a bit more heavy-handed than nature intended, and the targets of such coercion have a mechanism to overcome the new threat to their existence. Every microbe has in its arsenal of weaponry an “invisibility cloak” known as resistance genes, when activated the microbe can no longer be affected by the antibiotic signalling molecules.
Also intriguing is the discovery that antibiotics signal other microbes to form biofilms to protect themselves from invaders. When used indiscriminately, antibiotics administered in large doses signal the creation of biofilms by pathogens and they become nearly impossible to eradicate.
“Quorum Sensing” is used by microbes to signal an attack on a weakened immune system. Pathogens also talk to each other and when they detect they are in sufficient number to mount an impressive assault they go into “swarm mode” rapidly reproducing and moving to areas of immunocompromised tissues to completely overwhelm host defenses. Naturally produced antibiotic microbes are used to block the quorum sensing molecules, allowing a few probiotic species to fend off entire armies of pathogens. Man-made antibiotics can actually do the reverse, they can create a situation in which the quorum sensing molecules are heightened and the friendly, protective commensal species are all dead or diminished, leaving the host defenseless against a major microbial coup.
Prior to the age of man-made antibiotics, antibiotic resistance was a fact-of-life for billions of years. Microbes with active antibiotic resistant genes have been found in deep underground caverns and in populations of people and animals who have never encountered modern, man-made antibiotics, suggesting that antibiotic resistance is a natural occurrence.
Antibiotic resistance genes likely evolved for the following situations:
- Detoxify the host from antibiotics produced by it’s microflora
- Biosynthesis of the cell wall
- Trafficking of signaling molecules
- Detoxification of metabolic intermediates
- Extrusion of plant-produced compounds
What is missing from this list is “preservation of pathogens,” but this is exactly what we have done by applying mega-dosed antibiotics to microbes.
Microbes bombarded with a chemical meant to be a friendly deterrent soon become resistant to its effects. The original antibiotics have become impotent against many human pathogens, for years this was seen as a challenge that was readily accepted by the drug companies, now with resources nearly exhausted and “superbugs” entrenched in our midst, the age of antibiotics may soon come to a screeching halt.
Dr. Norm Robillard, microbiologist, Founder of the Digestive Health Institute, and author of the Fast Tract Digestion IBS and Heartburn book series, spent part of his career studying the mechanisms underlying antibiotic resistance. Robillard says of antibiotic resistance:   
Some bacteria are intrinsically resistant to many antibiotics, typically because they are able to prevent antibiotics from getting through their cell membrane. Others become resistant to antibiotics either by spontaneous mutation(s) in their own genes or by acquiring new antibiotic resistance genes from other bacteria.
Special thanks to Dr. Grace Liu, PHARMD, from Animal Pharm for contributions to this article.
Most resistance mutations act through alterations in various bacterial targets of antibiotics such as DNA gyrase, ribosomal proteins, or cell wall proteins. Most transmissible resistance genes act either by: decreasing permeability to antibiotics, deactivating the antibiotic through enzymatic cleavage or by providing efflux mechanisms that pump the antibiotic out of the cell.
Resistance genes are quickly acquired by bacteria because they are carried by a variety of transmissible genetic elements such as plasmids, transposons or viruses. There are three basic mechanisms by which bacteria are able to transfer resistance genes to one another:
1. Conjugation. Bacteria use rod-like appendages called pili as a shuttle for genetic material. I used conjugation quite a bit during research studying the ability of antibiotic resistance genes to move from E. coli strains in to Bacteroides fragilis strains. That work was the first time anyone ever moved antibiotic genes residing on a transmissible genetic element called a transposon, from E. coli to the strictly anaerobic B. fragilis.
2. Transformation. Bacteria have the ability to take up and incorporate foreign naked DNA. When one cell dies releasing its DNA, another bacterium can take that DNA up. Sometimes when this happens, the receiving bacteria incorporated the DNA into its own DNA completing the transfer of any traits on the donor gene.
3. Transduction. Bacteriophage (viruses that infect bacteria) sometimes package host DNA in error during their infection and infect new bacteria with genes from original host bacteria. With selective pressure such as antibiotics, it's easy to select for the resistant bacteria that have received the resistance gene in this manner. It's a common means used in microbial genetics labs to get genes from one strain to another. I used transduction to conduct genetic mapping in Bacillus strains including B. thuringiensis and B. anthracis.
Antibiotic resistance may or may not weaken the newly resistant bacteria, and in some cases the resistant bacteria undergo compensatory mutations as a way to deal with potential deleterious antibiotic resistance mutations. Also, resistance often requires the bacteria to expend extra energy to remain resistance. Examples include antibiotic-inactivating enzymes and efflux pump types of resistance.
The key effect of becoming antibiotic resistant is the bacteria is able survive in the presence of antibiotics while the others die off. In the gut, this results in a less diverse microbiota and less diverse microbiome (the latter is less threatening due to so much genetic redundancy in the microbiome). But the loss of microbiota diversity absolutely makes us more vulnerable to pathogen infection. That's the reason C. diff or yeast infections often follow antibiotic treatment.
 Martínez, JL. "Natural Antibiotic Resistance and Contamination by ..." 2012. <http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3257838/>
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