The Human Microbe Metropolis

E. coli, as an example, is very common in the human digestive system. We all have it. The so called good strains of e.coli pump out vitamin K₂ and may prevent other, more harmful strains from taking hold simply by being there. To expand on this idea, these good strains prevent the bad strains from getting a “foothold” simply by occupying all available “real-estate.”

Also, in the h. pylori example above, studies indicate that woman who harbor this bug and give birth through the birth canal (rather than by caesarian section) have much fewer instances of necrotizing enterocolitis in their newborns.  There are no hard studies to explain this, but observation indicates there must be a relationship no matter how weak.

This begs the question. Is playing host to colonies of these two bacteria actually preventative in some way? To date there is no hard research to back up these claims, but observation indicates there is some relationship between reduced incidents of fatal infections and having “good” versions of these bugs present. It will be up to science to determine just how that happens.

Bacteria have also been implicated in stubborn weight gain. Cursory studies have found that people who just cannot seem to keep the weight off have a overabundance of bacteria types called firmicutes. Laboratory mice which have been bred with no bacteria at all then “infected’ with firmicute type bacteria, experience sudden weight gain. A control group of mice, who lacked these types of microbes and were fed exactly the same diet, maintained normal weight. Are firmicutes somehow able to make digestion and nutrient extraction more efficient?

On the opposite end of the diet scale scientists have also discovered that people who have an overabundance of bacteroidetes seemed to be able to eat any amount and or type of food with weight gain impunity. This has also been borne out with rodent studies similar to the study mentioned above.

The “magic bullet” of the last century was the advent of antibiotics. Before the arrival of penicillin and its close cousins, the only way to treat an infection was with toxins such as mercury (syphilis), arsenic (gonorrhea), and sulfur (skin infections). These were effective, but could be quite deadly to some people. In fact, doctors and drug manufacturers using these compounds worked under the umbrella of “acceptable risk.”  For a compound to be effective a certain percentage of the population would very likely die from the treatment. The goal then was to keep that death toll to an acceptable minimum.

Antibiotics, in the form of fungus based compounds (like penicillin), changed that ratio dramatically. There are still deadly reactions to these drugs, but these reactions are a much smaller fraction compared to the reactions before. Fungal based antibiotics are also much more effective.

The problem, as science is now finding out, is that the broad-spectrum antibiotics, (called penams and cephams) kill off all bacteria; good, bad, or benign. In some cases this leaves a void where more deadly versions of microbes can re-infest and take hold, crowding out any potential “good” bacteria. As you might imagine this leaves the patient in a precarious state.  One specific example is in the repeated use of antibiotics to treat deadly infections such as heart value infections or pneumonia. Over time, these antibiotic courses wipe out the more benign versions of bacteria, making room for a bug called Clostridium difficile. C. difficile creates an intestinal infection that causes chronic diarrhea.  The only path of treatment is yet another course of antibiotics which does not always work.

The H. pylori bug is in rapid decline in the developed world with only six percent of the population still hosting it. This means an overall reduction in gastric ailments, but also seems to go hand in hand with an increase in asthma and esophageal reflux (heartburn).  To date h. pylori cannot be singled out as the agent responsible for preventing asthma or chronic heartburn, but there is a correlation. It is possible that another bacterium that peacefully coexists with h. pylori helps to prevent allergies and reflux. Perhaps h. pylori “trains” the immune system to be more tolerant, no one really knows. But this is an excellent example of how wiping out a bug for good reasons may results in less than desired results.

We are now painfully aware that repeated and unwarranted use of antibiotics lead to proliferation of super-bugs, bacteria that are resistant to all antibiotic treatment, but there are other risks as well.

A class of antibiotic called fluoroquinolones can cause tendonitis and tendon rupture. Achilles tendon rupture is four times more common in people taking fluoroquinolones. This prompted an FDA “black box” warning in labeling. Commercial names for this antibiotic are Cipro and Levaquin.

Azithromycin, marketed as Zithromax or Zmax (commonly administered as Z-Pak) has been linked to an increase in heart disease. Z-Pak has also been linked to irregular heart rhythm.

Antibiotic use in children has been linked to rashes, stomach ache, and diarrhea. Continual use has also been linked to Candida  overgrowth which, in turn, is linked to life-long problems with headache, acne, eczema, PMS, athlete's foot, cancer, allergies, depression, chronic fatigue, vision problems, sinus problems, ear problems, yeast infections, mood swings, irritable bowel syndrome, constipation, poor memory, chronic pain, and acid reflux disease. The root cause of this “overgrowth” seems to be the wiping out of bacteria that prevent Candida from taking over in the first place.

Antibiotics we don’t take also cause problems. The meat industries in particular (beef, pork, and poultry) routinely use antibiotics to affect the weight of their animals. Sub-therapeutic doses of antibiotics help these animals to gain more weight.  Though no one knows precisely why this happens, farmers take advantage of the fact. Also, antibiotics insure that more animals make it to market. But the potential for adverse effects in humans is high. Bacteria that survive on this meat are resistant to human antibiotic treatment.

Pork: In, February 6, 2002, a study published by the New England Journal of Medicine, indicated that there may be a link between people who develop Cipro resistant bacteria and their consumption of pork contaminated with flouroquine resistant salmonella.

Poultry: Baytril is a drug commonly administered to turkey. The problem begins when a veterinarian finds some indication of e. coli in the flock. Since it is impractical and expensive to treat one bird, the entire flock is given this drug in its water supply; a preventative and sub-therapeutic dose combined.  Because baytril is a sister drug to Cipro the possibility of creating drug resistant salmonella is very real. (Consumers Union reported just this problem and was roundly criticized for it.) The result, though inconclusive, indicate an increase in people with campylobacter infections that are resistant to drug treatment.

Beef: Micotil and Resflor are the two most common antibiotic drugs given cattle. They are not approved for human use and in fact Micotil can cause heart attacks while Restflor can cause bone marrow growth suppression. As with pork and poultry, these drugs are given cattle to forestall illness and help them gain weight.

To date the cattle industry denies a link between human illness and the consumption of beef. The industry insists that a veterinarian can test the cattle for antibiotic residue and reject an entire beef lot if any is found. But that does not address the concern of potential colonies of super-bugs that were created by treating the cattle with antibiotics. These reports also do not mention that the FDA is seriously understaffed, that veterinarians and feed lot owners determine whether or not to test, and enforcement of these rules is entirely up to the cattlemen or feed lot. In other words the industry is self-regulated.

In this section we look at using less or fewer antibiotics. In no way is it suggested you never use them, only that if you do use antibiotics, use them responsibly.

People need to be more aware of the dangers of “overmedication” and the complications this causes. Remember, a doctor is charged with curing ills, for that reason he or she may prescribe an antibiotic simply because you’ve asked for one, even if that prescription is against the doctor’s better judgment.

You can also avoid antibiotics in your food by carefully reading the label on your meat products. A label clearly marked “no antibiotics – ever” is now showing up on meats sold at Whole Foods. Other retailers who have sworn off antibiotic treated meat include; Giant, Hannaford, Shaw's, and Stop & Shop.

By federal law, any uncooked meat labeled “USDA Organic,” must be free of all antibiotics and hormones.

Labeling that uses terms such as “Natural,” “Antibiotic-free,” “No Antibiotic Residue,” or “No Antibiotic Growth Promotants” are meaningless. None of these designations have any connotation in the law and are therefore deceptive.

Scientists are beginning to promote the idea of a healthy and balanced microbial universe. This means no antibiotics and a natural balance of “probiotics” or “good” bacteria. To that end a number of new start-ups have incorporated to explore the possibilities of coming up with viable alternatives to antibiotics.

One program, called “American Gut”, invited top scientists in the field to submit flora (another word for microbial life) and have that microbial life thoroughly analyzed for $99. There was even a package for couples called “Microbes for Two” which invited pairs of participants to have their flora analyzed for $189. This could even be you and your dog (or cat). Participants would get a printout listing all of the microbes they harbor.

Another startup called “uBiome” was created to address such questions as “what happens to the biome in the presence of alcohol” and “does a vegetarian diet change the biome?” This particular effort is “crowd-funded.” One of the founders began collecting daily fecal samples from his newborn son to answer the question “what progression does the biome go through in the first year of life.”

“American Gut” and “uBiome” are warehousing all of the data collected from their programs and  making that data available to researchers.

“Second Genome”, founded by Peter DiLaura, is setting out to find alternatives to chemically derived antimicrobials. The company’s stated mission is to find “microbiome modulators” that alter infection, immunity, and metabolic disease.

The Republic of Karelian is just due east of Finland. Because of their geographic locations both Finland and Karelian share the same climate and environment. Due to the break-up of the Soviet Union Karelian is markedly different than Finland economically as well as in standards of living.

Life-style factors are also noticeably different between the two countries.  Finns, by and large, live much more hygienic life-styles compared to their Karelian neighbors. This includes exposure to microbial flora, the rate of infection, and treatment for those infections.

To determine what the differences in cleanliness levels might produce, the Department of Virology, University of Tampere, Finland, set out to determine the levels of hepatitis A virus, enterovirus, H. pylori and T. gondii infections. The study also set out to determine the differences in the number of incidents of allergic reaction in the total population of each country.

For consistency, The University of Tampere studied two hundred sixty-six children from each country; a total of five hundred thirty-two children. The children were chosen at random, but with the following two exceptions. Children from both countries were chosen by ethnicity such that both groups had similar ethnic backgrounds.  Children chosen for study were also between seven and eleven years of age.  Both groups were given blood tests to measure microbial load throughout the study. The children’s doctors were charged with keeping detailed records of each individual’s health.

U. of T. Finland findings are that the children from Russian Karelian had much higher incidences of H. pylori and T. gondii infection. These two bacteria are typically used as indicators of poor hygiene. The higher the bacterial load of these two microbes the less hygienic the children’s surroundings.

So far test results indicate that children with earlier exposure to these microbes are less sensitive to allergens. Specifically reactions to birch pollen and cat dander were measured in both groups. Finnish children become progressively more sensitive to pollen and animal dander as well as have more instances of asthma and hay fever.  The Karelian children’s reactions to these allergens remained flat.

Though these findings show a correlation between microbial load and allergic reaction they do not establish a cause and effect.

This field of research is relatively new.  It wasn’t until 1999 that there was any indication that we played “home” to so many microbes. There are also now doubts about H. pylori. Maybe it isn’t the real culprit in ulcers and stomach cancer. Perhaps it simply gives the real cause easy access to the stomach lining. Not all doctors agree; some insist that “the only good h. pylori is a dead h. pylori,” but there is little doubt that there is some correlation between harboring this so called bad flora and a reduction in allergic reactions in studied populations.

Science simply does not know the exact mechanism at play.

Because there are now known to be so many more bacteria than originally imagined it is going to take time, creative research, and enormous databases, along with the associated computing power, to sort out what is really going on.

That said, there is little doubt that our dependence on antibiotics is a two-edged sword. They have made previously deadly microbes little more than an annoyance. But, we have also inadvertently created stronger microorganisms, some that are completely resistant to all forms of treatment.

This poses a very frightening possible future. One in which we get revisit the bad old days of “kill or cure” or the time when previously minor infections could kill.

As of now there are no firm answers on what constitutes “good” bacteria or “bad” bacteria, but we do now have some tantalizing clues to work from.