“Germs make us sick, but everyone focusses on the harm.
And it’s not that simple, because without most of these organisms,
we could not survive.”
– Martin Blaser, MD; Professor of Microbiology, NYU School of Medicine
Bacteria (bugs) on and in our body outnumber our own cells by about 10 to 1. They only comprise 1-3% of our total body mass or up to about 3 pounds. but they essentially make life possible, as well as occasionally cause us great harm. That bacterial crowd, with its companions of fungus, protozoa other one-celled critters, is called a microbiome (“microbes that share our body space”). We inherit about 23,000 genes from our parents. Our microbiome contains 4 MILLION, and they are always working.
The National Microbiome Project funded by NIH for $115 million and completed in 2012 confirmed many associations between our bacteria and both health and illness. By our bacteria I mean “our” bacteria. Each person develops a unique microbiome starting with maternal bacteria received during birth. By age three years our microbiome is stable, but can be altered by antibiotics, what we eat, and sanitation practices. The “microbiome fingerprint” of an individual’s stool is distinct and can correctly identify a second stool from that same individual a month later 80% of the time.
Most of the bacteria we live with reside in our intestines. Roughly 70-80% of our feces is made up of bacteria living peacefully in our gut helping us to digest food, absorb sugar, protecting us from auto-immune disease, and maybe even to communicate with our brain. Certain groups of gut bacteria in mice have been shown to affect the blood-brain barrier, to make it more open, “to leak”, which has spurred some researchers to study the effect of gut bacteria on mental health. Associations between obesity, diabetes, and auto-immune diseases like Crohn’s and Irritable Bowel Syndrome (IBS) and the gut microbiome in laboratory mice have already been made.
Some gut bacteria in mice have been found to have two different, interchangeable physical shapes which can sense the environment (the kind of food passing by) and change from one shape to the other, just like a silicon chip. Crohn’s disease was long thought to be an infections disease, but is now considered a non-infectious inflammatory disease. In fact, the absence of one particular bacteria in mice reproduces Crohn’s disease symptoms in them. Human clinical researcher of the microbiome is flourishing.
Balance within our microbiome is important. Clostridium difficile, a pathogen when it overgrows in our gut when competing bacteria are knocked out by prolonged use of antibiotics, can cause debilitating diarrhea, dehydration, malnutrition, and even death. “Clostridial clusters”, a group of non-pathogens, on the other hand can detect sugar in the gut, increase insulin sensitivity, and may protect against the development of diabetes. The recently developed treatment of performing fecal transplants from healthy people to patients with C. difficile infections might be more readily accepted if we called them “microbiome transplants”.
Antibacterial soaps containing triclorsan have been found to be no more antibacterial than soap and water after 40 years of study reviewed by the FDA. Because of recent concerns about the effect of triclorsan on hormone levels and the growth of drug-resistant bacteria in lab animals, the FDA will require manufacturers to prove that their anti-bacterial soap or cleanser is better than soap and water or change its claims or cease its sale by 2016. Anti-bacterial solutions (Purell) are effective because they contain alcohol.
A recent study of the treatment of acute appendicitis with antibiotics alone (24 hours of high dose IV and then 10 days of oral antibiotics) has shown that in selected cases that non-operative treatment is as successful as surgical treatment. Long-term follow-up of these patients remains to be done.
The microbiome of the subway was studied in 2013 by Weill Cornell Medical School investigators who collected and analyzed hundreds of DNA samples from the underbelly of New York City. The good news is that very few samples had the DNA of disease-causing bacteria, and only 1% was identifiable as human bacterial DNA. The more striking fact is that “48% of the DNA found did not match any known organism”. Now, the investigators say that’s because our databases of genomes are incomplete, but I think that there is a Stephen King novel waiting to be written there.
1. Scientific American, June 2012,, The Ultimate Social Network, Jennifer Ackerman
2. Scientific American, Feb, 2015, Innovations In, The Microbiome
3. Weill Cornell Medicine, Vol. 14, No. 1
4. New Yorker, Oct. 22, 2012 p.32, “Germs Are Us” by Michael Specter
5. Microbes can be used to identify individuals, Boston Globe, May 18,2015, B4