In the spirit of All Hallow’s Eve, we have our own spooky story to tell about what creatures might be lurking inside each of us – but rest assured: this haunting tale has a happy ending.
The gut microbiome is known to have quite a bit of diversity, with up to a thousand different species of bacteria calling your digestive system their home. These bacterial strains range from Firmicutes and Bacteroidetes – our predominant companions – but we also have Proteobacteria, Verrucomicrobia, Actinobacteria, and many others as well. Beneficial bacteria work in extravagant ways to maintain their home and stabilize the gut ecosystem, and they’re incredibly resilient creatures that have survived the earliest days of life, though they’re not alone in our gut.
When we refer to our “microbes,” we mean bacteria, yes, but we also mean fungi, archaea, protists, and viruses. Most interestingly, many of the viruses inside our gut microbiome don’t infect our human cells at all – rather their prey is more focused on the bacteria that thrive inside us. This makes bacteriophages – or viruses intent on bacteria – an interest to scientists seeking alternatives to deadly, antibiotic-resistant microbes.
A Worldwide Epidemic
The first antibiotic was created in 1928 by a Professor of Bacteriology called Alexander Fleming, purely by accident.  Dr. Fleming was studying a series of bacteria that were known to cause boils, sore throats, and abscesses, though his hope to find a cure seemed continually thwarted. Upon returning from vacation, however, one of his bacterial petri dish colonies seemed to show signs of death where mold had been growing on it. This discovery lead to what we now refer to simply as penicillin, a rare but naturally occurring fungi that inhibits bacterial growth.
Since then, several other antibiotics have been discovered and used to treat a wide variety of bacterial infections.  This has saved countless lives and helped doctors treat common issues from strep throat to frightening cases of flesh-eating bacteria. However, the over-prescription of strong antibiotics in cases that could have been resolved with a softer touch, overuse, antibiotics used in farming practices, and lack of new drug development have all helped to create new strains of highly resistant bacteria. 
For example, Staphylococcus aureus is a common bacteria found on our skin. Normally, this bacteria remains harmless, however, in certain conditions, it can break out and become a highly infectious pathogen. With the overuse of antibiotics, small cases of staph have become diagnosed as MRSA, a common concern in hospitals around the world.  MRSA stands for Methicillin-resistant Staphylococcus aureus and is extremely difficult to eliminate. What's more, as we continue to use antibiotics to treat MRSA, some microbiologists speculate it may become near impossible.
For many scientists, this marks the beginning of new superbugs that may penetrate into human populations. Superbugs are bacteria that are so antibiotic-resistant, that seemingly benign infections can turn into untreatable cases. Some estimates put drug-resistant diseases could kill 10 million people a year by 2050.  Moreover, as we continue to explore the far reaches of our planet – scientists are concerned with what prehistoric super-microbes we might uncover.
Caped Crusader or Bacterial Boogeymen?
It’s no surprise, then, that the world must take innovative new steps to combat the rising wave of man-made bacterial evolution. Some scientists have found a promising new field of research in developing highly specific bacteriophages that infect pathogenic bacteria, destroying them from the inside out (the word bacteriophage literally means bacteria
Although you might initially think of them as a new Superman to your Superbug Villain, a closer look at these eerie figures under a strong microscope might raise the hair on the back of your neck. Their elongated alien-like heads and sharp claws seems more like something from a Stephen King novel than your favorite Marvel action movie.
What’s even spookier is how they do it, and it’s not for the faint of heart.
Insert, Replicate, Devour
Just like the M.O. for many human viruses, bacteriophages work in very similar ways as they infect bacteria.
Many bacteriophages contain a head, a tail, and their own claw-like machinery to attach on to the surface of a bacteria. On the outside, they contain specific antigens that act like microscopic keys that work with locks only found on specific bacterial membranes. This high-level specificity is one of the many astounding traits that make bacteriophages so fascinating to scientists. By manipulating these antigens, researchers believe they can meticulously code for specific bacterial strains with razor-sharp precision, a process that is becoming a strong possibility for the future.  These antigens connect perfectly with these “lock” receptors on their bacterial prey, and then they quickly attach themselves by clamping down with razor-sharp talons.
Once attached, a sliver of DNA or RNA is injected into the bacteria, where it combines with the bacteria’s genetic code. Soon enough, the bacteria’s own replication software begins creating copies of the virus instead of itself and stopping normal tasks. Soon, the bacteria fills up until its bursts, releasing thousands more of the same bacteriophage into the environment, ready to find their next victim. 
A haunting tale, indeed, but one that shows a lot of exciting potential against the warring tides of antibiotic resistance.
In truth, this may become the way of the future. Although scientists are still working to develop highly specialized bacteriophage viruses that only harm the pathogen in mind without harming other microbes helpful to us (just like in our gut microbiome), they might be closing in on a breakthrough.
Only time will tell, but the potential remains.
Hopefully, stories of hard to treat infections will be told like old-fashioned ghost stories, where the bacteriophage plays the role of the bacterial boogeyman – or perhaps these microscopic organisms really are like hidden heroes of scientific folklore.
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